when the final rank list is made for jee main 2020 and if the best of two percentile is taken. but when the rank is calculated they consider total number of students. For ex: if 10 lakhs have written on the jan atmpt this time only around 6 lakhs have written which number of stu will they consider?

The higher percentile is considered to calculate rank. If you score the higher percentile in January attempt, that will be taken into account to calculate your rank. Now as the students appearing in September is less than January, they will obviously get a higher rank compared to the students appeared in January attempt. Rank is calculated using following formula:

Rank = (100 - percentile) * total number of students appeared / 100