维基百科说:

MinGW forked from version 1.3.3 of Cygwin. Although both Cygwin and MinGW can be used to port UNIX software to Windows, they have different approaches: Cygwin aims to provide a complete POSIX layer that provides emulations of several system calls and libraries that exist on Linux, UNIX, and the BSD variants. The POSIX layer runs on top of Windows, sacrificing performance where necessary for compatibility. Accordingly, this approach requires Windows programs written with Cygwin to run on top of a copylefted compatibility library that must be distributed with the program, along with the program's source code. MinGW aims to provide native functionality and performance via direct Windows API calls. Unlike Cygwin, MinGW does not require a compatibility layer DLL and thus programs do not need to be distributed with source code. Because MinGW is dependent upon Windows API calls, it cannot provide a full POSIX API; it is unable to compile some UNIX applications that can be compiled with Cygwin. Specifically, this applies to applications that require POSIX functionality like fork(), mmap() or ioctl() and those that expect to be run in a POSIX environment. Applications written using a cross-platform library that has itself been ported to MinGW, such as SDL, wxWidgets, Qt, or GTK+, will usually compile as easily in MinGW as they would in Cygwin. The combination of MinGW and MSYS provides a small, self-contained environment that can be loaded onto removable media without leaving entries in the registry or files on the computer. Cygwin Portable provides a similar feature. By providing more functionality, Cygwin becomes more complicated to install and maintain. It is also possible to cross-compile Windows applications with MinGW-GCC under POSIX systems. This means that developers do not need a Windows installation with MSYS to compile software that will run on Windows without Cygwin.

Cygwin使用兼容层，而MinGW是本地的。这是主要的区别之一。

Cygwin模拟整个POSIX环境，而MinGW是仅用于编译的最小工具集(编译本地Win应用程序)。所以，如果你想让你的项目跨平台，MinGW显然是两个选择之一。

尽管你可能会考虑在Windows上使用VS，在Linux/ unix上使用GCC。大多数开源项目都这样做(例如Firefox或Python)。

Cygwin使用一个DLL, Cygwin . DLL，(或者可能是一组DLL)在Windows上提供类似posix的运行时。

MinGW编译为本地Win32应用程序。

如果您使用Cygwin构建某个东西，那么您安装它的任何系统也将需要Cygwin DLL。MinGW应用程序不需要任何特殊的运行时。

维基百科在这里做了一个比较。

来自Cygwin网站:

Cygwin是一个用于Windows的类似linux的环境。它由两部分组成:DLL (cygwin1.dll)，作为Linux API模拟层，提供大量的Linux API功能。 提供Linux外观的工具集合。

摘自Mingw网站:

MinGW(“Minimalistic GNU for Windows”)是一个免费提供和可自由分发的Windows特定头文件和导入库的集合，结合了GNU工具集，允许人们生成不依赖任何第三方C运行时dll的本地Windows程序

为了补充其他答案，Cygwin附带了MinGW库和头文件，你可以在不链接到cygwin1.dll的情况下使用-mno-cygwin标志与gcc进行编译。比起使用普通的MinGW和MSYS，我更喜欢这个。