Objective To investigate the content of thorium (Th) in surface water in Sichuan Province, China, and to evaluate Th-associated health risk via water intake for residents. Methods Twenty-three monitoring sections were set in main surface water bodies in Sichuan Province. From 2016 to 2021, the Th radioactivity level in the water bodies was measured during dry and normal-water seasons. The health risk of residents was evaluated by calculating radioactive Th intake from the surface water bodies combined with the use of a health risk assessment model. Results The Th radioactivity level of the surface water bodies in Sichuan Province was 0.02-0.67 μ./L. There was no significant difference in the Th radioactivity level of different years or different surface water bodies (P > 0.05). A significant difference was observed in the Th radioactivity level of different water seasons (P < 0.05). The total mean annual committed effective doses of Th in all age groups caused by drinking water and water immersion ranged from 3.14 × 10⁻⁸ to 8.75 × 10⁻⁷ Sv, all lower than the World Health Organization (WHO)-recommended reference level of 0.1 mSv. The overall carcinogenic risks for residents in all age groups ranged from 3.93 × 10⁻¹⁰ to 1.09 × 10⁻⁸, all below the most rigorous control limits issued by WHO and International Commission on Radiological Protection. Conclusion The Th-associated health risk via direct water intake and water immersion in main surface water bodies of Sichuan Province is at an acceptable level. Th in main surface water bodies of Sichuan Province is safe for all age groups.