NCERT textbooks of 11th and 12th standard of Physics, Chemistry and Mathematics are a must. Along with them the best reference books for JEE Mains are as follows :-

For Physics :-

• Concepts of Physics by HC Verma Volume 1 and Volume 2
• Problems in General Physics by I. E Irodov 
• Fundamentals of Physics by Halliday, Resnick and Walker
• Objective questions on physics by D. C Pandey 
• Advance Physics by Nelkon and Parker 

For Chemistry :- Chemistry is divided into three sections as follows-

Physical Chemistry :-

• Physical Chemistry by O. P Tandon 
• Numerical Chemistry by R. C Mukherjee 
• Physical Chemistry by P. W Atkins

Organic Chemistry :-

• Organic Chemistry by O. P Tandon
• Organic Chemistry by Morrison and Boyd 
• Organic Chemistry by T. W Solomons 
• Concept of Organic Chemistry by M. S Chauhan

Inorganic Chemistry :-

• Inorganic Chemistry by O. P Tandon 
• Concise Inorganic Chemistry by J. D Lee

For Mathematics :- 

• Mathematics Class 11th and 12th by R.D Sharma 
• Trigonometry by S. L Loney
• Co-ordinate geometry by S. L Loney 
• Higher Algebra by Hall and Knight
• Problems in Calculus of One Variable by I. A Maron
• Algebra by Arihant publications 
• Differential Calculus by Arihant publication. 

A student is not supposed to refer every book. 2-3 books for each subject are fine. Also a previous year question papers book can be referred to be familiar with types of questions that come in examination. 

If you still have any queries feel free to ask in the comment section down below.