If I do not get my OBC certificate at the time (before the jee mains result) then am I consider as a general student? because I changed my general (January) category to OBC (spetember) and which percentile is counted January or September ?

As you have noted yourself as an OBC category candidate in the application form of Jee Main, you have to provide proper documents to support your statement. And if you are unable to provide your OBC Caste certificate during counselling, your candidature will not be cancelled but you'll be no be considered for admission under OBC category. You'll be automatically transferred to general category and your general rank would be considered for admission to engineering colleges. If you have applied and appeared for both the sessions of Jee Main - i.e. January and September, best of the two marks will be considered for admission.