Objective To quantitatively evaluate the relationship between the raw-freshwater fish-eating practice and the infection of Clonorchis sinensis. Methods Total 16 counties were enrolled from 4 provinces highly endemic with clonorchiasis (Guangxi, Guangdong, Heilongjiang and Jilin), and 5 villages were selected from each investigated counties as survey sites. Total 200 residents from each site were recruited for the investigation. The fecal samples were collected from each participant and the eggs of C. sinensis in the feces were examined under microscope using Kato-Katz thick smear method, and the information on eating raw freshwater fish among the participants was collected. The linear relationship between the percentage of participants eating raw freshwater fish and the prevalence of C. sinensis infection was analyzed in people living in different counties, with different genders and age. The parameter of coefficient of determination (R²) was determined accordingly. The relative risk (RR) and 95% confidential intervals (95% CI) were calculated for those with raw-freshwater fish-eating practice compared to those without the practice. Subsequently, attributable risk (AR), attributable risk percent (ARP), population attributable risk (PAR) and population attributable risk percent (PARP) were analyzed. Results A total of 16 230 participants from 16 counties were enrolled in this survey. The percentage of participants with practice of eating raw freshwater fish was 26.5% (4 295/1 6230) and the overall prevalence of C. sinensis infection was 10.8% (1 747/1 6230) with a positive linear association between them in investigated counties (R² = 0.44, P < 0.01). The percentage of eating raw freshwater fish was 31.7% (2 687/8 478) in males and 20.7% (1 608/7 752) in females (P < 0.01), while the corresponding prevalence of C. sinensis infection was 13.7% (1 161/8 478) and 7.6% (586/7 752) (P < 0.01). The percentage of eating raw freshwater fish in males aged ≤14, 15-29, 30-44, 45-59 and ≥60 was 1.9%, 19.4%, 40.2%, 44.5% and 36.3%, respectively, positively correlating with the prevalence of C. sinensis infection of 1.5%, 7.5%, 15.1%, 20.8% and 15.4%, correspondingly (R² = 0.96, P < 0.01). The percentage of eating raw freshwater fish in females aged ≤14, 15-29, 30-44, 45-59 and ≥60 was 2.3%, 13.9%, 25.3%, 29.2% and 22.4%, correspondingly, with positive linear association with, the prevalence of C. sinensis infection of 1.2%, 6.1%, 9.0%, 10.4% and 8.0%, respectively(R² = 0.99, P < 0.01). Compared to those without the practice, RR of C. sinensis infection in those with the practice reached 12.9 (95% CI: 11.4-14.7). RR was 11.8 (95% CI: 10.0-14.0) in males and 13.4 (95% CI: 10.9-16.4) in females between eating raw freshwater fishes and the chance of getting infected. RR ranged from 8.2-16.1 in different age groups. Overall, AR for eating raw freshwater fishes and the infection of C. sinensis was 30.9%, ARP was 92.3%, PAR was 8.2%, and PARP was 75.9%. In males, AR was 33.5%, ARP was 91.5%, PAR was 10.6% and PARP was 77.4%, compared to those in female of 26.2%, 92.5%, 5.4% and 72.0%, respectively. AR ranged between 15.6% and 34.0%, ARP between 87.9% and 93.8%, PAR between 0.3% and 12.7%, and PARP between 24.1% and 79.7% in different age groups. Conclusion Raw-freshwater fish-eating practice is seriously associated with the infection of C. sinensis and the difference in raw-freshwater fish-eating practice determines the different distribution of C. sinensis infection in areas and population in these investigated endemic areas.