Which is tougher, the KVPY or the JEE Main?

• JEE Advanced put emphasis on numerically challenging questions, which is not the case for KVPY. However, KVPY and JEE Advanced require a similar amount of conceptual clarity.
• KVPY aims to test your subject knowledge.  Whereas JEE usually tests the numerical ability of students in core Mathematics, Physics, and Chemistry.
• Very few students clear both examinations. As the expectations of the students taking these examinations are different. 

Both KVPY and JEE Main are difficult but in different ways.