Objective To explore the effects of chromosome polymorphism on the pregnancy outcome of assistant reproductive treatment. Methods The peripheral blood chromosome detection was conducted for 5 345 infertile couples who underwent the assistant reproductive treatment. The process of assistant reproduction of 3 435 periods was retrospectively analyzed. Patients with chromosome polymorphism were selected, divided into groups according to different types, and then compared to normal people. The fertilization rates, cleavage rates, rates of effective embryo formation, accumulated pregnancy rates, and early abortion rates were observed. Results Compared to the control group, the differences of fertilization rates, cleavage rates, rates of effective embryo formation, accumulated pregnancy rates, and early abortion rates of the polymorphism group, Y chromosome variation group, 1/9/16 variation group, and D/G variation group were not statistically significant (P>0.05), but the difference of cleavage rates of pericentric inversion of chromosome 9 was statistically significant (P<0.01). The differences of all other indexes were not statistically significant. Conclusion The pregnancy outcome of patients with chromosome polymorphism is not significantly different from normal people after the assistant reproductive treatment.