If you're at a significant height and reach disadvantage, there are several things you need to do:
First, as everyone else has said, you live by your jab. This is true for everyone, but especially shorter guys; you will need to jab to get inside. Use good footwork, circle away from their power and move your head when he gets close. Use feints.
Second, as someone else said- make them chase you. If you're drawing them in, then they're coming forward, meaning that you have control over when you're going to explode in and close the distance. When moving forward, they give up a certain amount of reach/ reaction time because of momentum. The second that they look frustrated or overextended, that's when you pounce in: jab to get inside, then blast them with hooks & uppercuts, and finish with a leg kick.
If you're fighting a really patient counterstriker who refuses to hunt you down, it becomes a bit more interesting. Use a lot of side to side movement, especially with your head. Use feints try try and elicit a response/ counter- this is what people are talking about when they say "counter the counterfighter". And when you finally do hunt them down, make them pay for running. Overpower them in exchanges, put your fists on their jaw and your shins into their thigh. Make them fight ugly, because they HATE fighting ugly.