Can I report my math GPA instead of major (CS and math) GPA when applying to graduate school? So I'm a combined Math/CS major wanting to do grad school for pure math. My GPA my first 3 semesters was terrible, and I got my shit together after that.

While I have all A's in math courses, my major GPA would include CS courses as well, and those are my worst grades. I estimate I can't raise it above 3.5 by next December.

I would like to know if I have any flexibility in how I report my GPA, i.e. if I can report a math GPA instead of a major GPA.
Report the GPA they ask for. Anything else is basically fraud.

If you're unclear what GPA they require, look up their requirements, and contact them if necessary to ask. They may allow you to do your major GPA, or they may require your overall GPA. They may allow just your Math GPA.

At some point they're going to see your whole transcript, so there's no way to "hide" your past. But, many applications have a section for you to explain extenuating circumstances, where you could explain that you had difficulty with the CS materials and excelled at math.