Abstract Chinese hamster with Chinese characteristics is used in experiments, and it is of great value in the field of medical biology research. However, at present, there is no high‐efficiency method for evaluating the genetic quality of Chinese hamsters. Here, we developed a novel Chinese hamster genetic quality detection system using single‐nucleotide polymorphism (SNP) markers. To find SNP loci, we conducted whole genome sequencing on 24 Chinese hamsters. Then, we employed an SNP locus screening criterion that we set up previously and initially screened 214 SNP loci with wide genome distribution and high polymorphism level. Subsequently, we developed the SNP detection system using a multitarget region capture technique based on second‐generation sequencing, and a 55 SNP panel for genetic evaluation of Chinese hamster populations was developed. PopGen.32. analysis results showed that the average effective allele number, Shannon index, observed heterozygosity, expected heterozygosity, average heterozygosity, polymorphism information, and other genetic parameters of Chinese hamster population A were higher than those in population B. Using scientific screening and optimization, we successfully developed a novel Chinese hamster SNP genetic detection system that can efficiently and accurately analyze the genetic quality of the Chinese hamster population.