Raw or undercooked meat is an important source of Toxoplasma gondii infection in China, but there is little research data on these infections in Chongqing. This study determined the prevalence of T. gondii, and its genotypes, in pork. A total of 1,223 diaphragm muscle samples were collected from eight slaughterhouses and 79 markets and detected by PCR amplification of the ITS gene. All of the positive samples were used for genotype identification by PCR-RFLP with 11 genetic markers. The total positive rate of T. gondii in Chongqing pork was 8.7%, and differences in T. gondii infection rates were found between different districts (0%–23.3%), seasons (e.g., 4.3% from Spring, 7.3% from Summer, 11.4% from Autumn, 12.0% from Winter) and years (2.7%–14.3%). Six samples were successfully genotyped, of which one was identified as ToxoDB#9 and five were ToxoDB#9-like. This was the first continuous study about the prevalence of T. gondii in pork in Chongqing for several years. Slaughterhouses in different districts, pork source, farm scale, season and year were potential risk factors for T. gondii contamination by the univariate logistic regression, and using multivariate logistic regression districts, pork source and year were the independent risk factor. These data may help reducing the levels of toxoplasmosis in pigs and humans in Chongqing.