Do you know Who he is?能不能是Who do you know he is?.

1可以
2不可以
do you know在句中可以作为插入语，在1中，Do you know who he is/Who(do you know)he is意思一致
但2不可以，因为Do you think what it is的语法是错误的．

可以的，两句的DO you know 都是插入语
插入语既可以放在句前，也可以放在句中
类似的还有do you think

关于插入语，可以分为下面一些
1. 用简短的句子结构作插入语。这类短语有:I think, I hope, I guess, I believe, I suppose, I wonder, I tell you, I say, I'm afraid, I'm sure, you see, you know, as you know, that is, that is to say, what's more等等,它们可以置于句中或句尾。如:

I suggest you choose someone who you think is kind and friendly.

This diet, I think, will do good to your health.

It won't be raining long, I hope.

You will have to work harder, you know, if you want to succeed.

2. 副词或副词短语用作插入语,这类插入语一般放在句首或句尾。如:

Happily for him, his father's second wife was kind to him too.

You'll be able to pass the coming exam, surely.

Luckily for him, he didn't hurt in the accident.