Hello,

Here is the eligibility criteria for admission into IIT through JEE Main:-

1. Candidate should have qualified jee advance exam  to apply for counselling process
2. Students must have secured 75% aggregate marks in 12th exam. For reservation categories the percentage considered is 65% percentage.

This says that your all subjects are taken into consideration which means that if you have secured a percentage above 75% in 12th final year exam then only you can take part in counselling.

HSC percentage is not taken into consideration. Only 12th percentage is  kept in the eligibility criteria.

For more information please visit the link below:-

https://engineering.careers360.com/articles/jee-advanced-counselling-and-seat-allotment

Hope it helps!