Cardiovascular disease (CVD) has become an increased risk to human health, and the abnormal cholesterol metabolism will increase the risk of developing CVD. Along with the development of high-throughput sequencing technology and population genomics, the scanning for genes or mutations related to complex traits (or diseases) has been greatly promoted. Also, it becomes possible to explore the genetic mechanism of cholesterol metabolism. In this review, we summarize the progress of molecular genetic studies of cholesterol metabolism, based on the results of traditional genetic method and GWAS screening. Finally, the functional background of abnormal cholesterol metabolism was explored by pathway enrichment analysis. All these analyses will contribute to a better understanding of cholesterol molecular mechanism, and will also provide clues for prevention and treatment of cholesterol metabolism disorders.