Why do you call appendix as a vestegial organ when it has some functions?

There are several in the body. You are asking about the one attached to the colon (digestive tract)? This one is often called the vermiform appendix because it looks like a worm.

There are several ideas why we have these. Some say this is "left over" as we evolved. Others say that it is important in the way that the immune system works. The last group thinks that important and helpful bacteria are found here and repopulate the intestine after many are killed during an infection. No final conclusion has been reached.