Background: Clonorchissinensis, one of the most important food-borne zoonotic trematodes, remains prevalent in China. Understanding its infection status in animals is crucial for controlling human clonorchiasis. Here we conducted a systematic review and meta-analysis to focus on the spatio-temporal disparities of C.sinensis infection in animals in China. Methods: Data on C.sinensis prevalence in snails, the second intermediate hosts, or animal reservoirs in China were extracted from electronic databases including PubMed, Embase, Web of Science, Chinese Wanfang database, CNKI, VIP, and China Biomedical Literature database. A random-effects meta-analysis model was utilized to estimate the pooled prevalence in each of the above animal hosts. Subgroup analysis and multivariable meta-regression were performed to explore potential sources of heterogeneity across studies and compare the temporal disparity of infection rates between high and low epidemic areas. Scatter plots were used to depict the biogeographical characteristics of regions reporting C.sinensis infection in animals. Results: The overall pooled prevalence of C.sinensis was 0.9% (95% CI: 0.6–1.2%) in snails, 14.2% (12.7–15.7%) in the second intermediate host, and 14.3% (11.4–17.6%) in animal reservoirs. Prevalence in low epidemic areas (with human prevalence < 1%) decreased from 0.6% (0.2–1.2%) before 1990 to 0.0% (0.0–3.6%) after 2010 in snails (P = 0.0499), from 20.3% (15.6–25.3%) to 8.8% (5.6–12.6%) in the second intermediate hosts (P = 0.0002), and from 18.3% (12.7–24.7%) to 4.7% (1.0–10.4%) in animal reservoirs. However, no similar decrease in prevalence was observed in high epidemic areas (with human prevalence ≥ 1.0%). C.sinensis infections were predominantly reported in areas with altitudes below 2346 m and annual cumulative precipitation above 345 mm and were mostly concentrated in eastern China. Conclusions: There are spatio-temporal disparities in the animal infections of C.sinensis in different areas of China. Animal infections are primarily concentrated in regions with low altitude and high precipitation. The results suggest that implementing One Health-based comprehensive measures targeting both humans and animals, especially in high epidemic areas, is essential for successful eradication of C.sinensis in China.