宾语从句中，是I don't know what the matter is,还是I don't know what's the matter??

I don't know what is the matter. 对。
因为这里的what在从句中做的是主语，the matter是表语。也就是说what is the matter就是陈述句型，所以用在从句中是不需要改变顺序的。

I don't know what's the matter?

宾语从句中只有what's the matter是特例，不需要改为陈述语序。

I don't know what's the matter.

这里是主系表结构。what是主语，is是系动词，the matter是表语，符合陈述句语序，所以无须改动。

应该是I don't know what the matter is

因为是从句，所以 系动词 is 要提前```

比如：
应该是 i do not know who you are 。

而不是 i do not know who are you 。

I dont know what is the matter.
因为what这里是主语.不换顺序