I think "How long have you been working?" and "How long you have been working?" are both questions, so, could you tell me what is the difference between them?

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    The second is not a properly formed question, alternative might be "You have been working for how long?" – Peter Nov 27 '16 at 16:50

How long have you been working?

*How long you have been working?

The former is grammatical; it's a direct or normal question.

The latter has not been formed properly. If you omit the question mark, you can form an indirect question in indirect (reported) speech as follows:

He asked me how long I had been working.

To be more polite and formal, you can also form an indirect question in the following way:

Could you tell me how long you have been working?

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    "He asked me how long I have been working": this is wrong. You have so say "He asked me how long I had been working." – TonyK Nov 28 '16 at 12:05

They are not both questions.

"Have you" is part of a question:

Have you been working? How long?

"You have" is part of a statement:

You have been working. I know how long.

In a question without a question-word with "be," the subject and verb order change position to indicate that it is a question.

So, "How long you have been working?" is an error. A correct statement using that word order: "I'm amazed by how long you have been working!"

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I don't think either of the existing answers have covered this case. But the second form, you have could be used to express surprise at how long someone has been working.

A commonly told childrens story, Red Riding Hood, is usually told with some variation of this refrain:

My, what big ears you have!

What big eyes you have!

What big teeth you have!

It's a little archaic, now, and rarely used in common language, but this may be the intention of your initial sentence.

I just thought I'd try to help, because that's the kind of guy I am. ;)

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    Maybe expand your answer to clarify the correct archaic statement you are implying is possible based on OP language. I think you are suggesting: "My, how long you have been working!" – JeremyDouglass Nov 28 '16 at 17:29

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