This study was purposed to explore the influence of number and locus of HLA allele mismatch on unrelated donor hematopoietic stem cell transplantation (URHSCT) in Chinese Han population. Total 10 alleles within the HLA-A/B/C/DRB1/DQB1 loci were analyzed by PCR-SSP for 101 pairs of donor and recipients who received URHSCT. 101 cases of URHSCT were divided into four groups: HLA-allele 10/10 match (n = 30), 9/10 (n = 32), 8/10 (n = 31) and 7/10 match (n = 8). The correlation of the HLA with overall survival (OS ≥ 1 year), incidence of acute GVHD (aGVHD) of grade II to IV and relapse rate of primary diseases were evaluated. The results showed that (1) The OS rates in HLA-10/10 and 9/10 groups were higher than that in HLA-8/10 match group (78% and 82% vs 50%, p = 0.39); incidence of aGVHD in the HLA-10/10 were lower than that in HLA-9/10 and HLA-8/10 group (0% vs 10% and 10%; p = 0.28); relapse rates among the 3 groups were close (16%, 18% and 20%, respectively). Although there were only 8 cases in HLA-7/10 match URHSCT, the data indicated that they were safe and effective; (2) Compared to the HLA-10/10 match URHSCT (n = 30), the HLA-C mismatch URHSCT (n = 12) harbored higher incidence of severe aGVHD (0% vs 25%, p = 0.006), longer OS (77% vs 85%, p = 0.30), and tendency to low relapse rate (8% vs17%, p = 0.47); (3) According to HLA-C1/C2, the ligands of inhibitory KIR, the 42 cases of HLA-10/10 match URHSCT and HLA-C mismatch URHSCT were grouped into donor/recipient HLA-C1/C2 match and mis-match subgroups. There was no difference between the two subgroups for OS, incidence of aGVHD and relapse rate (78% vs 80%, 14% vs 20%, and 5% vs 20%). It is concluded that for 0 to 2 locus of HLA allele mismatch in URHSCT, the fewer mismatch numbers, the longer OS, but with similar aGVHD incidence and the relapse rate; triple HLA allele mismatch (HLA-7/10 match) is safe in URHSCT. The HLA-C mismatch may be related to higher incidence of aGVHD and lower relapse rate and prolonged OS, remaining to be further studied.