I see that there is an additional ~KRA file generated when I save my project as krita format. I want to ask what it is and whether I can delete it or not?

It is a copy of your file as it was before you saved it again -- so it's a sort of very limited version history. If you're sure you don't want to go back to the previous state, you can remove it. If you're sure you're never going to mess up and save an image with all layers deleted (say...) over your original image, you can even disable the creation of backup files in Krita's settings.