The genetic background of an individual is a crucial factor to be considered toward personalized medicine or PM. It is now very feasible to re-sequence an individual genome due to recent advances in DNA sequencing technologies (in particular, NGS). However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variation within and between populations. In this context, population genetics and genomics play a vital role in dissecting genetic architecture of complex traits/diseases by separating locus-specific effects from genome-wide effects. Nonetheless, considering very heterogeneous ethnic groups and large population size in China, great efforts are necessary to provide a more precise and comprehensive characterization of the genomic diversity of natural populations. Here, I will give a brief overview of our recent progresses in human population genetics studies in China, including the fine-scale genetic structure of the Han Chinese population, the largest ethnic group in the world, and that of some minority groups such as the Tibetan, the Uyghur, and Tujia populations.