How to handle the plagiarism on references? Recently I received a plagiarism report on my accepted manuscript. It is highlighted that total 25% text appeared in other sources though they are cited properly. 

When I checked the report, I found ~20% text appears in references only and another ~3% text is due to the use of a long phrase "The tropical cyclone wind speed climatology". This phrase was actually very frequently used in one of my another paper. The rest ~2% text appears in introduction and methods. In methods, I had used some well known mathematical equations and related descriptions e.g. which variable denotes what. 

So how to deal with this situation? How can I convince to the editor?
25% similarity is low. Similarity in references should also be discounted. I suspect it's either a mistake or something you don't have to pay attention to - you mention that your manuscript's already been accepted, and they might just be sending plagiarism reports with the acceptance email as a matter of course.

If the editor also said something like "please correct these plagiarized text", I'd write back saying that the similarities outside of the bibliography are minute, and ask for clarification.