子查询中的内部联接是不必要的。看起来您想要删除story_category中的条目，其中category_id不在类别表中。

而不是：

DELETE FROM story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category INNER JOIN
         story_category ON category_id=category.id);

执行以下操作：

DELETE FROM story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category);

DELETE FROM story_category
WHERE category_id NOT IN (
    SELECT cid FROM (
        SELECT DISTINCT category.id AS cid FROM category INNER JOIN story_category ON category_id=category.id
    ) AS c
)

如果Priority列值在表中大于等于1，并且在WHERE子句中使用同一表上的子查询，以确保至少有一行包含Priority＝1（因为这是在执行更新时要检查的条件），则我会这样做：

UPDATE My_Table
SET Priority=Priority + 1
WHERE Priority >= 1
AND (SELECT TRUE FROM (SELECT * FROM My_Table WHERE Priority=1 LIMIT 1) as t);

我知道它有点难看，但它确实很好。

就问题而言，您希望删除story_category中不存在于类别中的行。

以下是用于标识要删除的行的原始查询：

SELECT * 
FROM  story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category INNER JOIN 
       story_category ON category_id=category.id
);

将NOT IN与JOIN原始表的子查询组合在一起似乎不太复杂。这可以用不存在和相关子查询以更直接的方式表示：

select sc.*
from story_category sc
where not exists (select 1 from category c where c.id = sc.category_id);

现在很容易将其转换为delete语句：

delete from story_category
where not exists (select 1 from category c where c.id = story_category.category_id);    

这个quer可以在任何MySQL版本上运行，也可以在我知道的大多数其他数据库中运行。

DB Fiddle演示：

-- set-up
create table story_category(category_id int);
create table category (id int);
insert into story_category values (1), (2), (3), (4), (5);
insert into category values (4), (5), (6), (7);

-- your original query to identify offending rows
SELECT * 
FROM  story_category 
WHERE category_id NOT IN (
    SELECT DISTINCT category.id 
    FROM category INNER JOIN 
       story_category ON category_id=category.id);

| category_id |
| ----------: |
|           1 |
|           2 |
|           3 |

-- a functionally-equivalent, simpler query for this
select sc.*
from story_category sc
where not exists (select 1 from category c where c.id = sc.category_id)

| category_id |
| ----------: |
|           1 |
|           2 |
|           3 |

-- the delete query
delete from story_category
where not exists (select 1 from category c where c.id = story_category.category_id);

-- outcome
select * from story_category;

| category_id |
| ----------: |
|           4 |
|           5 |

对于OP试图实现的特定查询，理想且最有效的方法是根本不使用子查询。

以下是OP的两个查询的LEFT JOIN版本：

SELECT s.* 
FROM story_category s 
LEFT JOIN category c 
ON c.id=s.category_id 
WHERE c.id IS NULL;

注意：DELETE s将删除操作限制在story_category表中。文档

DELETE s 
FROM story_category s 
LEFT JOIN category c 
ON c.id=s.category_id 
WHERE c.id IS NULL;

试试这个

DELETE FROM story_category 
WHERE category_id NOT IN (
SELECT DISTINCT category.id 
FROM (SELECT * FROM STORY_CATEGORY) sc;