Thorium (Th) is a natural radioactive element present in the environment and has the potential to be used as a clean nuclear fuel. Relatively little is known about the aquatic toxicity of Th, especially in nanoparticulate form, which may be the main chemical species of Th in the natural waters. In this study, impacts of ThO2 nanoparticles (NPs) with two different sizes (52 ± 5 nm, s-ThO2vs. 141 ± 6 nm, b-ThO2) on a green alga Chlorella pyrenoidosa (C. pyrenoidosa) were evaluated. Results indicated that C. pyrenoidosa was more sensitive to s-ThO2 (96-h EC30 = 64.1 μM) than b-ThO2 (96-h EC30 = 100.2 μM). Exposure to 200 μM of ThO2 NPs reduced the chlorophyll-a and chlorophyll-b contents of the algal cells. At 96 h, SEM and TEM showed that more agglomerates of s-ThO2 than those of b-ThO2 were attached onto the surface of algal cells. Reactive oxygen species (ROS) generation and membrane damage were induced after the attachment of high concentrations of ThO2 NPs. The heteroagglomeration between ThO2 NPs and algal cells and increased oxidative stress might play important roles in the toxicity of ThO2 NPs. To the best of our knowledge, this is the first report on aquatic toxicity of ThO2 NPs.