The purpose of this study was to detect chromosomal aberrations and azoospermia factor (AZF) microdeletions in male patients with reproductive problems and to summarize related clinical features to provide reliable information for evaluating prenatal and preimplantation diagnoses. A large cohort of 5083 men with various phenotypes of male infertility was analyzed via G-banding karyotyping, and Origin 8.0 was used to analyze the prevalence of abnormalities. Additionally, patients with azoospermia, oligozoospermia, and oligoasthenozoospermia were analyzed using multiplex polymerase chain reaction to detect microdeletion in the AZF. We identified 387 patients with abnormal karyotypes, and the ratio was 7.61%. Among them were 175 patients with Klinefelter’s syndrome, which was the most common numerical chromosomal abnormality and accounted for 45.22% of all chromosomal aberrations. The frequencies of increased satellites, balanced translocations, and Robertsonian translocations were 6.47, 7.00, and 3.62%, respectively. Multiplex polymerase chain reaction performed in 810 cases with azoospermia, oligozoospermia, and oligoasthenozoospermia found a ratio of AZF microdeletions of 4.94%.