I assume the two sentences are
1) Do you know what is it?
2) Do you know what it is?
I kinda do a Google research on this and basically most people say it should be the first one but unfortunately the correct one is the second one.
Why it is so? If we refer to the rule of making question (WH-word + verb to be/verb to have + subject + verb + description). But based on the question above, there are no verb/description after the subject. So, now here the second rule (WH-word + subject + verb to be)
So, here you are. Based on the second rule the second one is right.
1) Do you know what is it? (Wrong)
2) Do you know what it is? (Right)
3) Do you know what is it all about? (Right, as there is a description behind the subject)