I have severe pain on my stomach, and the ultrasound and CT scan showed a cyst on my right ovary. I also have a endometriosis. Will the cyst go away?

Depends. It depends on what kind of cyst it is and how big it is. An endometriotic cyst may shrink with certain medications, but usually requires surgery. Simple cysts frequently resolve on their own, especially they are not large. There are many other types of cysts and rumors of the ovary that may require surgery.
No. If it is endometriosis then it will not go away. There are medical treatments to try to minimize pain but only surgery can remove it. It would be worthwhile to repeat an ultrasound right after your next period to see if it is still there. Just because you have endometriosis does not mean that every cyst is endometriosis.