Questions which are asked in JEE Main are based on NCERT only but some questions are of higher level. 

In chemistry there are around 60-75% questions directly from NCERT.

Mathematics is the hardest section to crack in JEE Main and you should refer other books as well.

In Physics the basics for most problems in JEE Mains are from NCERT textbook for Physics and all you require is to alter the arguements as required in the problem. 

To score good marks it is very important that your concepts should be clear.

With the help of NCERT books you can qualify JEE Main exam but you will not score good mraks.

To get good marks in JEE Main it is very important that you explore other books as well and solve previous year papers.

All the best!!