Abstract: Objective To analyze the relationship between small Y chromosome and oligospermia by analyzing relative length of chromosome. Methods Two hundred and six patients aged from 20 to 55 years who received chromosome karyotype analysis and had Y chromosome microdeletion in our hospital from December 2016 to December 2017 were selected, and they were divided into abnormal sperm group (n=142) and normal sperm group (n=64). Then the length of Y chromosomes relative to 21 chromosome were measured by BEION chromosome analysis software, and the Y chromosome with relative length less or equal to the length of 21 chromosome were identified as small Y chromosome. The proportion of small Y chromosome was compared between two groups. Results There were 20 (14.1%) out of 142 samples with small Y chromosome in abnormal sperm group, and 7 (10.9%) out of 64 samples in normal sperm group, with no significant difference between the two groups (P＞ 0.05). Conclusion There is no correlation between short Y chromosome and oligospermia.