A, in 20 13, the mathematics scores of ninth-grade students in Kunming were overall, and the original statement was wrong, so option A was wrong;

B, every ninth-grade student's math scores are individual, and the original words are wrong, so option B is wrong;

C, 1000 ninth-grade students' math scores are a sample of the whole, and the original statement is wrong, so option C is wrong;

D, the sample size is 1000, which is correct, so the D option is correct.

So choose D.