DYS549, DYS527, and DYS459 loci, located on the azoospermia factor (AZF) region and widely used in forensic and pedigree analysis, may be specifically altered in infertile patients, which will obscure the result of individual identification using Y-STR (Y chromosome short tandem repeat). In this study, we determined the AZF polymorphism by STS(-/-) (sequence tagged site) and DAZ, CDY1 gene copy numbers, and screened the samples by 14 Y-STR loci to disclose the unusual genotype of Y-STR in male infertility population. The 240 infertile males including non-obstructive azoospermia, severe oligozoospermia and congenital bilateral absence of vas deferens (CBVAD) were analyzed with a modified multiplex PCR system for AZF microdeletion STSs. AZF microdeletions were found in 40 cases (16.67%) (AZFa deletion, two cases; AZFb deletion, two cases; AZFc deletion, 30 cases; AZFb+c deletion, six cases). Further screening by the 14 Y-STR loci in samples with microdeletions, we found DYS549 allelic loss in all the cases with AZFb deletion, DYS527 and DYS459 allelic loss in all the cases with AZFc deletion, DYS549, DYS527, and DYS459 allelic loss in all the cases with AZFb+c deletion. Ten patients (4.17%) with AZFc partial duplication (one CBVAD case, two non-obstructive azoospermia cases, seven severe oligozoospermia cases) were found by DAZ and CDY1 gene dosage analysis. In conclusion, the unusual patterns of DYS549, DYS527, and DYS459 are caused by genetic defects rather than experimental bias. Revealing the locus heterogeneity in male infertility population can enrich the Y-STR database and assist in interpreting abnormal STR genotype in forensic DNA testing.