For me it was feelings of depression and worthlessness. Sometimes I did it because I felt so bad and when I hurt myself it made me feel better. Other times I did it because at the time I did not like myself. Have you tried talking to a professional that has experience in this?

I talked to a school counselor that didn't help very much, and a psychiatrist who gave me medications, which I didn't find very effective. I eventual found a psychologist that dealt with childhood trauma/neglect and she was able to help sort some of the emotions/thoughts out. At least until my insurance ran out. It helped me to talk to someone who wasn't judgmental and could help me figure out what I got out of it and better ways to cope. After talking to her I felt less messed up and more like someone who is trying to deal with overwhelming emotions. I hope this helps you.