You have to build your aerobic base.
You have to work in the easy zone and stay there. Long slow distance, even walking is fine will build you aerobic system base.
There's two rules out there. one is Maffletones, which is stay below 180-your age = HR. This is really low, but it does work.
the other one is find your VT1, it's the HR where talking becomes uncomfortable. Below this HR you can talk pretty comfortably, above this, you can talk, but in much shorter pieces. Get on a treadmill with a HR monitor (the hands work) and go a little faster every 2 minutes and say the pledge of allegiance. You'll know when you reach it. Record your VT1, stay below that marker. It should (and probably will) be higher than the Maffletone HR.
But part of it is that your body is doing a LOT of work, running a big body is a lot of work.
Fat people shouldn't run, find something else to do as cardio that isn't so taxing on your joints.