NCERT books helps to clear your basics and to build your fundamentals strong. You should refer NCERT books to complete your syllabus as it is based on NCERT only. If you want to score good marks in JEE Main you should refer previous year  papers to understand the exam pattern and level of questions. Focus on the important topics you can solve MCQs related to them. You should also solve complete mock test series to analyze your preparation level at regular interval of time.

Apart, from NCERT you can also go through below recommended books

Physics

Concepts of Physics Vol I and II by H.C. Verma

Fundamentals of Physics by Halliday, Resnick & Walker

Problems in General Physics by I.E. Irodov

Mathematics

Maths XI & XII by R.D. Sharma

Plane Trigonometry Part 1 by S.L. Loney

Plane Co-ordinate Geometry by S.L. Loney

Higher Algebra by Hall and Knight

Problems in Calculus of One Variable by I.A. Maron

Chemistry

Physical Chemistry by O.P. Tandon

Organic Chemistry by Paula Bruice Yurkanis

Organic Chemistry by Paula Bruice Yurkanis

NCERT books will help you to build your fundamentals strong. But if you want to score good marks you have to follow other recommended books as well.

Other books you can prefer. Other books you can prefer.

Physics
HC Verma – Concepts of Physics (Part I)
HC Verma – Concepts of physics (Part II)
IIT JEE Physics – DC Pandey
Problems in General Physics – I.E. Irodov
Physics for IIT-JEE- Resnick, Halliday, Walker.
Problems in Physics- S.S. Krotov

Chemistry
Organic Chemistry – Morrison Boyd
Organic Chemistry – O.P Tandon.
Modern Approach to Chemical Calculations – R.C. Mukherjee
Numerical Chemistry – P. Bahadur
Concise Inorganic Chemistry – J.D. Lee

Maths
IIT Mathematics – M.L. Khanna
Differential Calculus – A Das Gupta
Class XI & XII Mathematics- R.D. Sharma.
Trigonometry, Geometry Books- S.L. Loney.
Problems in Calculus of One Variable- I.A. Maron
Higher Algebra- Hall and Knight

Good Luck!