I am currently confused between the use of these two:
Does it worth all the trouble?
Is it worth all the trouble?
Can some one suggest which one is correct?
Worth may be a noun or an adjective, but not a verb. In your context it is a predicate adjective, almost invariably employed with BE:
This house is worth one million dollars.
It is worth the trouble.
Consequently, you cannot use DO here--there's no verb to act as its complement.
The common idiomatic phrase is "Is it worth X?" or even the seemingly tautological "Is it worth it?" In this case you have to figure out the meaning of the pronouns from context. For example:
Buying a home can be a difficult, frustrating, and ultimately expensive process -- plus, afterwards, there are all the headaches the comes with home ownership. Is it worth all that trouble?
Joining the military is a serious commitment that should not be taken lightly. Before you let yourself be pressured into enlisting, you should ask yourself, "Is it worth it?"
As others have pointed out, "worth" is not a verb and so you can't ask "Does it worth it?" However can you use the standard "to be" verb to say things like:
Does it seem like it would be worth the trouble?
Does it look like a good investment that is worth the cost?