How to interpret 本质 here? When I look up 本质 I get English meanings like 'essence, nature， innate character', esoteric stuff like that.

学习必须讲究方法，而改进学习方法的本质目的，就是要提高学习效率。

I think 本质 here actually means 主要， 最初 and 本质目的 is 'primary aim'.

Could I use 主要 here instead of 本质 and not affect the original meaning?
本质 here means root; ultimate. 

本质目的 = end goal. You can also say 根本目的.

Your sentence sounds fine but isn't the best example to demonstrate usage, because it's kind of obvious. A better example might be:


  商业活动的本质目的是盈利。The end goal for any commercial activity is making profit.