Y-chromosome short tandem repeats (Y-STRs) loci have significant research and application value in individual identification, parentage testing, kinship determination and genealogical DNA analysis due to their unique genetic characteristics. Currently, various commercial STR typing kits have used in forensic detection, which greatly promoting the scientific application of STR in criminal investigation and judicial trials. However, due to the complexity and specificity of biological samples, the special STR typing in the sample poses certain difficulties for the construction of DNA databases. In the current study, we explored the Y-STR genotyping in 4670 unrelated individuals using the Yfiler™ Platinum Kit, AGCU Y37 and AGCU Mini Y fluorescence detection kit in the Henan Province. We found that eight samples had inconsistent typing results. Among them, the genotyping inconsistency occurred twice for the Y_GATA_H4 locus, and once each for the loci DYS481, DYS444, DYS635, DYS437, DYS533 and DYS570. We sequenced and analyzed the inconsistent loci of these samples. Sequencing results indicated inconsistent typing due to low polymorphic repeat structures, Poly(N)n structures, single or multiple base insertions/deletions, and base transitions or transversions in flanking regions. Special attention should be paid to using the Y-STR database for family searches and paternity testing.