使用jdom2: http://www.jdom.org/

import java.io.StringReader;
import org.jdom2.input.SAXBuilder;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;

String prettyXml = new XMLOutputter(Format.getPrettyFormat()).
                         outputString(new SAXBuilder().build(new StringReader(uglyXml)));

这是我自己问题的答案。我将各种结果的答案结合起来，编写了一个输出XML的类。

不保证它如何响应无效的XML或大型文档。

package ecb.sdw.pretty;

import org.apache.xml.serialize.OutputFormat;
import org.apache.xml.serialize.XMLSerializer;
import org.w3c.dom.Document;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.Writer;

/**
 * Pretty-prints xml, supplied as a string.
 * <p/>
 * eg.
 * <code>
 * String formattedXml = new XmlFormatter().format("<tag><nested>hello</nested></tag>");
 * </code>
 */
public class XmlFormatter {

    public XmlFormatter() {
    }

    public String format(String unformattedXml) {
        try {
            final Document document = parseXmlFile(unformattedXml);

            OutputFormat format = new OutputFormat(document);
            format.setLineWidth(65);
            format.setIndenting(true);
            format.setIndent(2);
            Writer out = new StringWriter();
            XMLSerializer serializer = new XMLSerializer(out, format);
            serializer.serialize(document);

            return out.toString();
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
    }

    private Document parseXmlFile(String in) {
        try {
            DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
            DocumentBuilder db = dbf.newDocumentBuilder();
            InputSource is = new InputSource(new StringReader(in));
            return db.parse(is);
        } catch (ParserConfigurationException e) {
            throw new RuntimeException(e);
        } catch (SAXException e) {
            throw new RuntimeException(e);
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
    }

    public static void main(String[] args) {
        String unformattedXml =
                "<?xml version=\"1.0\" encoding=\"UTF-8\"?><QueryMessage\n" +
                        "        xmlns=\"http://www.SDMX.org/resources/SDMXML/schemas/v2_0/message\"\n" +
                        "        xmlns:query=\"http://www.SDMX.org/resources/SDMXML/schemas/v2_0/query\">\n" +
                        "    <Query>\n" +
                        "        <query:CategorySchemeWhere>\n" +
                        "   \t\t\t\t\t         <query:AgencyID>ECB\n\n\n\n</query:AgencyID>\n" +
                        "        </query:CategorySchemeWhere>\n" +
                        "    </Query>\n\n\n\n\n" +
                        "</QueryMessage>";

        System.out.println(new XmlFormatter().format(unformattedXml));
    }

}

下面是一种使用dom4j的方法:

进口:

import org.dom4j.Document;  
import org.dom4j.DocumentHelper;  
import org.dom4j.io.OutputFormat;  
import org.dom4j.io.XMLWriter;

代码:

String xml = "<your xml='here'/>";  
Document doc = DocumentHelper.parseText(xml);  
StringWriter sw = new StringWriter();  
OutputFormat format = OutputFormat.createPrettyPrint();  
XMLWriter xw = new XMLWriter(sw, format);  
xw.write(doc);  
String result = sw.toString();

为了将来的参考，这里有一个对我有用的解决方案(感谢@George Hawkins在其中一个答案中发表的评论):

DOMImplementationRegistry registry = DOMImplementationRegistry.newInstance();
DOMImplementationLS impl = (DOMImplementationLS) registry.getDOMImplementation("LS");
LSSerializer writer = impl.createLSSerializer();
writer.getDomConfig().setParameter("format-pretty-print", Boolean.TRUE);
LSOutput output = impl.createLSOutput();
ByteArrayOutputStream out = new ByteArrayOutputStream();
output.setByteStream(out);
writer.write(document, output);
String xmlStr = new String(out.toByteArray());

嗯…面对这样的事情，这是一个已知的bug… 只需添加这个OutputProperty ..

transformer.setOutputProperty(OutputPropertiesFactory.S_KEY_INDENT_AMOUNT, "8");

希望这对你有所帮助……

以上所有的解决方案都不适合我，然后我找到了这个http://myshittycode.com/2014/02/10/java-properly-indenting-xml-string/

线索就是用XPath删除空格

    String xml = "<root>" +
             "\n   " +
             "\n<name>Coco Puff</name>" +
             "\n        <total>10</total>    </root>";

try {
    Document document = DocumentBuilderFactory.newInstance()
            .newDocumentBuilder()
            .parse(new InputSource(new ByteArrayInputStream(xml.getBytes("utf-8"))));

    XPath xPath = XPathFactory.newInstance().newXPath();
    NodeList nodeList = (NodeList) xPath.evaluate("//text()[normalize-space()='']",
                                                  document,
                                                  XPathConstants.NODESET);

    for (int i = 0; i < nodeList.getLength(); ++i) {
        Node node = nodeList.item(i);
        node.getParentNode().removeChild(node);
    }

    Transformer transformer = TransformerFactory.newInstance().newTransformer();
    transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
    transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
    transformer.setOutputProperty(OutputKeys.INDENT, "yes");
    transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");

    StringWriter stringWriter = new StringWriter();
    StreamResult streamResult = new StreamResult(stringWriter);

    transformer.transform(new DOMSource(document), streamResult);

    System.out.println(stringWriter.toString());
}
catch (Exception e) {
    e.printStackTrace();
}