Non-classical human leukocyte antigen (HLA)-DM plays an important and unique role in the processing and presentation of exogenous antigens. Polymorphisms of certain genes and frequency of alleles in populations may indicate susceptibility to certain diseases. In this study, the analysis of HLA-DMA and HLA-DMB gene polymorphisms and haplotypes in the Chinese Han population was conducted to obtain population genetic data. HLA-DM typing has been performed previously by other groups by polymerase chain reaction (PCR)-restriction fragment length polymorphism and PCR-sequence-specific oligonucleotide probe techniques. In this study, we established a Taq Man PCR typing method as an alternative to these techniques to survey the frequency of DMA and DMB alleles in the population. Genotyping was conducted in 1000 unrelated individuals of Han nationality in South and North China using Taq Man PCR typing. Four different DMA alleles and six different DMB alleles were detected. All loci met the Hardy–Weinberg equilibrium principle that both allele and genotype frequencies in a population remain constant. We found that the DMA*01:01 (69.35%) and DMB*01:01 (52.5%) alleles were more frequent in Chinese Hans. Analysis of the haplotypes for two loci of DMA and DMB showed that a highly significant positive linkage disequilibrium (LD) presented for DMA*01:01–DMB*01:02, DMA*01:01–DMB*01:03, DMA*01:01–DMB*01:04, DMA*01:02–DMB*01:01, DMA*01:02–DMB*01:05, DMA*01:03–DMB*01:07, and DMA*01:04–DMB*01:01 haplotypes. Analysis of haplotypes for four loci associated with antigen processing (DMA–DMB–TAP1–TAP2) showed a highly significant LD in DMA*01:01–DMB*01:04–TAP1*02:01:01–TAP2*01:02, DMA*01: 02–DMB*01:05–TAP1*01:01–TAP2*01:01, and DMA*01:01–DMB*01:03–TAP1* 04:01–TAP2*01:01 haplotypes. The comparison between the Chinese Han population and non-Chinese populations showed that no significant differences were found at the HLA-DMA locus in the Chinese Han population compared with people of German nationality, whereas significant differences presented when compared with Turkish, American Caucasian, Japanese, French, and Italian nationalities. However, at the HLA-DMB locus, highly significant differences presented in the Chinese Han population compared with Germans and Italians. This study lays the foundations for further disease association analyses.