Cerebral small vessel disease (CSVD) is an important cause of stroke and cognitive impairment, with complex pathogenesis and limited therapeutic options. Although monogenic hereditary CSVD has a low incidence, its well-defined causative genes provide a unique " natural model" for revealing the core molecular pathways of CSVD. Based on previous studys, this article systematically sorts out the newly identified pathogenic genes of monogenic CSVD, such as NIT1, MAP3K6 and ARHGEF15, and precisely identifies core pathophysiological processes including vascular smooth muscle cell dysfunction and extracellular matrix homeostasis imbalance. Furthermore, it reviews the latest advances in genome-wide association studies (GWAS) on sporadic CSVD and its imaging markers, and confirms an overlap in their genetic architectures. Finally, this article discusses the research strategy of integrating multi-omics data such as transcriptomics and proteomics to deeply analyze the biological mechanisms of risk variants, and summarizes the clinical translational value of genetic research in the precision diagnosis, risk stratification, drug target mining and drug repositioning of CSVD.