首先我们来看下what are you doing和what you are doing的大致意思：
what are you doing：词性为短语，what: 什么；are: 是（be动词的现在进行时）；you: 你；doing: 做（动词do的现在分词形式）
what you are doing：词性为短语，what: 什么；you: 你；are: 是（be动词的现在时）；doing: 做（动词do的现在分词形式）
通过下面的表格我们了解下what are you doing和what you are doing的含义、发音和用法
接下来让我们看下what are you doing和what you are doing的用法区别：
1.语法结构：what are you doing是一个完整的疑问句，而what you are doing是一个宾语从句
例子：
- What are you doing?
(你在做什么？)
- I want to know what you are doing.
(我想知道你在做什么。)
2.用法场景：what are you doing常用于询问对方当前的行为，而what you are doing常用于引导宾语从句，在正式场合或书面语中更常见
例子：
- What are you doing?
(你在忙什么？)
- The teacher wants to know what you are doing.
(老师想知道你正在做什么。)
3.口语 vs 书面语：what are you doing更常用于口语交流，而what you are doing更常用于书面语和正式场合
例子：
- What are you doing?
(你在干嘛呢？)
- I want to know what you are doing.
(我想知道你正在做什么事情。)
4.语序：what are you doing的语序为疑问句语序，而what you are doing的语序为陈述句语序
例子：
- What are you doing?
(你正在做什么？)
- Tell me what you are doing.
(告诉我你正在做什么。)