Unfortunately, there is not much you can do to prevent conceiving twins if you are taking Clomid. It is one of those side effects that will determine whether or not you want to take the medication, just like mood swings, possible cramping and bleeding, and other possible Clomid side effects. Some women actively welcome the possibility of multiples, and there are even those who take Clomid just to increase their chance of having twins when they don't have any actual fertility problems. Short of "selective reduction", an IVF euphemism for aborting one or more of the babies when high-order multiples are conceived, there is nothing you can do once you opt to use Clomid to conceive.
Incidentally, the "risk" of conceiving multiple babies is not limited to Clomid alone, and is also associated with IVF, the other popular fertility treatment. If you are unsure what the risks of a twin pregnancy are and you are afraid of conceiving multiples because of the risks that would pose to your health and the babies', you may want to discuss these aspects of a twin pregnancy with your doctor before you commence taking Clomid. You may find that twin pregnancies are not as risky as you assumed in most cases, and that you would not mind conceiving twins after all! With good prenatal care and monitoring, most twin pregnancies are healthy.