I use implanon, lately started getting irregular periods and pain around ovary region with swelling on one side of lower stomach, is it a cyst?

Likely: The irregular periods are not uncommon when using Implanon. Pain or swelling would not be a side effect of Implanon. A large ovarian cyst may cause swelling of the abdomen in addition to pain. I assume you've had this pain for several weeks or more. If by chance the pain just started within the past 1-2 days, and is severe, you could have a ruptured cyst or ovarian torsion and should go to the ER