You receive a certain amount of score for killing a red dot or collecting a powerup. This value increases by differing amounts depending on whether or not you killed a dot, or collected a powerup, and is the first number in the set. Of note is the fact that different power ups give you different scores.
The second number is the score multiplier, and increases by 1 every time you do either, within the time-out limit of the combo.
Therefore, in the example below:
[ COMBO 48 x 3 ]
'48' is the base score you have received from your heroic actions over the course of that particular multiplier, but before multiplication. The '3' represents your current multiplier. If you fail to continue the combo in a short enough amount of time, that is what your current combo score (48) will be multiplied by, and the combo ended.