Objective Construct a Y chromosome haplogroup Single Nucleotide Polymorphism multiplex system (Y-SNP system) and evaluate its application value in familial searching of forensic genetic. Methods The Y-SNPs that widely distributed in East Asia were screened. The system was constructed based on capillary electrophoresis (CE) genotyping platform, and its performance and accuracy were evaluated and verified. 20 male samples from four pedigrees were collected. And the genotypes of Y-SNP and Y Chromosome Short Tandem Repeat, (Y-STR) genetic markers were performed using the Y-SNP system and DNA TyperTM Y29 kit respectively. The differences of haplogroups and haplotypes in each pedigree were analyzed, and the network was used to visualize the mutation. Results A total of 74 Y-SNPs were selected and constructed in double-tube of multiplex system. The SNP genotypes obtained by Y-SNP system were completely consistent with Sanger sequencing results. The low DNA detection limit was 0.14ng. In addition, this system was suitable for blood stain, oral swabs, nails, hair root. Except chimpanzees and rhesus monkeys, there was no specific peak in non-human DNA samples. In P1 pedigree, the Y-SNP haplogroups and Y-STR haplotypes of samples were identical. In P2 pedigree, the Y-SNP haplogroups of all samples were identical and Y-STR haplotypes were different (mismatched loci ≤5). In P3 pedigree, the Y-SNP haplogroups of all samples were different and Y-STR haplotypes were different (mismatched loci >5). In P4 pedigree, the Y-SNP haplogroups of all samples were identical and Y-STR haplotypes were different (mismatched loci >5). Conclusion The combination of Y-SNP and Y-STR can improve the accuracy of familial searching.