This study is based on 75 Y-SNPs and 23 Y-STRs to analyze the paternal genetic structure of Shandong Han and Hui males and provides basic data for forensic application and population genetics. Mini-sequencing was used to type 75 Y-SNPs of 187 individuals of Han and 130 individuals of Hui. The PowerPlex^®Y23 kit was used to type 23 Y-STRs of all individuals. Allele frequency, haplotype frequency and haplogroup frequency were calculated by direct counting. Gene diversity, haplotype diversity and haplogroup diversity were calculated according to the formula D=n(1-∑pi²)/(n-1). The median-joining networks were constructed using NETWORK 5.0 and NETWORK Publisher. The research results showed that haplogroup O-M175, C-M130, N-M231, Q-M242 were the major haplogroups of the Han population, and haplogroup O-M175, J-M304, R-M207, C-M130, N-M231 were the major haplogroups of Hui population. 187 haplotypes were detected in Han populations based on twenty-three Y-STR loci, and the haplotype diversity was 1.000. And 121 haplotypes were detected in Hui populations, the haplotype diversity was 0.9988. The Networks showed that the individuals of same haplogroup were relatively independently clustered. There were shared haplogroups between Han and Hui populations, as well as some population specific haplogroups. For example, haplogroups J-M304 and R-M207 were prevalent in Hui population, while haplogroup Q-M242 was prevalent in Han population. The major haplogroup of both populations was haplogroup O-M175. Haplogroups J-M304 and R-M207 were distributed at high frequencies in Shandong Hui male population, and haplogroups Q-M242 were distributed at high frequencies in the Shandong Han male population. A certain percentage of unique Y chromosome haplotypes in western Eurasia and the Middle East were retained among the Shandong Hui male population.