A, Mendel's paired genetic factors refer to alleles, and different pairs of genetic factors refer to non-alleles on non-homologous chromosomes, and A is wrong;

B, Mendel thinks that YyRr plants can produce four kinds of female gametes and four kinds of male gametes, which are yr, yR, Yr, YR respectively, and the ratio is1:1.B is correct;

C, the variation of alleles on homologous chromosomes cross-exchanged by non-sister chromatids in tetrad stage belongs to gene recombination, and C is wrong;

D the chromosome number of human cells is 2N in the process of subtracting Ⅰ, n in the early, middle and late stages of subtracting Ⅱ, and 2N in the late stage of subtracting Ⅱ. D is wrong.

Therefore, choose: B.