What is the difference between "How it works?" and "How does it work?"?
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In these examples each question is preceded by a statement in the indicative mode, with the constituent to be moved in [brackets]. In the question, _ represents the normal position of the constituent which the interrogative replaces, and ∅ stands for an absent or deleted constituent in the 4 or 5 position. When the statement contains no auxiliary verb, the appropriate form of do is inserted in the question; this is bolded in the question.
When you encounter a construction in which the interrogative is followed by a noun or pronoun you are not dealing with a question but with a free relative clause. In this construction, the constituent which the interrogative represents is moved to the head of the clause, but there is no rearrangement of the subject and verb: these follow in their ordinary, indicative order. The verb may include an auxiliary but it is not required to have one. Clauses of this sort are not questions; they are not even complete sentences. They act as NP (nominal) constituents within a sentence. The interrogative represents the head of the clause, and the remainder of the clause in effect ‘defines’ that head as if it were an ordinary restrictive relative clause.
In these examples the statement is transformed into a free relative clause, which is shown in [brackets] within a sentence. The ordinary position of the constituent which the interrogative represents is, as before, shown with _.
† Forms of BE are always treated as auxiliaries for this purpose, so if the BE form is the main verb it is not repeated in this fourth position, as in sentence C1. Until quite recently forms of HAVE worked the same way, but this use is dying.
'How it works' used in an interrogative phrase is something you may not find very commonly spoken amongst native speakers.
But then again, it may be a part of an interrogative sentence, as in:
Here, 'how it works' is correct because it isn't a direct part of the question being asked. The question asked is, "Will you tell me _?" 'How it works' is just that part of the sentence which goes into the blank, as an assertive phrase.
'How does it work' is what you'd say while asking somebody about the way it works. This construction is used in interrogative sentences.
I'll correct Maulik's second answer:
You see that he sets the expressions in context, which is always very important.
If you're using a sentence fragment rather than a sentence proper in your first example (say as a section heading), you'd drop the question mark (and probably the period):