Everyone’s eyes water when they yawn. Some people just have more prominent watering of the eyes. The watering of the eyes when you yawn is because of your lacrimal glands and the glands’ ducts.
Tears are created in the lacrimal glands in order to protect your eyes from becoming dry. It is kind of like your mouth creating saliva so you don’t have a constant dry mouth. Tears are constantly being processed, although some actions force the glands to process more at certain times; such as when you cry. An overproduction of tears (like when crying) can also make your nose run because the ducts actually connect to your nasal passages.
Perhaps you have an issue with dry eye and your glands are doing extra work and producing extra tears to protect your eye. When you yawn, the pressure could be releasing these extra tears. Regardless, you are not the only one who has this issue. It is actually quite common and normal. If you are very concerned about this problem, talk to your doctor (or ophthalmologist) about your concerns.
Reference: http://www.lasikmd.com/blog/eyes-water-yawn/