The distribution of human leucocyte antigen (HLA) allele and haplotype varied among different ethnic populations. In this study, we investigated the allele and haplotype frequencies of HLA-A, HLA-B and HLA-DRB1 loci in the Nanning Han population who live in Guangxi province of China. We identified 26 HLA-A, 56 HLA-B and 31 HLA-DRB1 alleles in 562 Nanning individuals of Han ethnic group by sequence-based typing method. Of these, the three most common alleles in HLA-A, HLA-B and HLA-DRB1 loci, respectively, were A*11:01 (32.12%), A*02:07 (12.54%), A*24:02 (12.01%); B*46:01 (14.41%), B*15:02 (13.61%), B*40:01 (11.48%); DRB1*15:01 (14.15%), DRB1*16:02 (11.57%) and DRB1*12:02 (10.14%). With the exception of HLA-DRB1, the p values of the HLA-A and HLA-B loci showed that the HLA allelic distribution in this population was in accordance with Hardy-Weinberg expectation (p > 0.05). A total of 173 HLA~A-B~DRB1 haplotype with a frequency of >0.1% were presented and the three most common haplotype were HLA-A*33:03~B*58:01~DRB1*03:01 (6.12%), HLA-A*11:01~B*15:02~DRB1*12:02 (3.39%) and HLA-A*11:01~B*15:02~DRB1*15:01 (3.22%). The phylogenetic tree and the principal component analysis suggested that Nanning Han population had a relative close genetic relationship with Chinese Zhuang population and a relative distant genetic relationship with Northern Han Chinese. The information will be useful for anthropological studies, for HLA matching in transplantation and disease association studies in the Chinese population.