Toxic effects on Asterococcus superbus were studied based on different combinations of P25-TiO2, nano-ZnO and triclosan under multiple illumination conditions. A full factorial design (2 × 2×2 × 3) was implemented to explore interactive effects, and to identify significant factors. The results showed illumination is the most important factor with significance and becomes one of the main reasons to affect chlorophyll pigments, photosynthesis activity, unsaturated fatty acids, mitochondria function, and cause oxidative stress. Triclosan considerably affects cell viability, photosynthesis activity, lipid peroxidation and protein structure, for which triclosan is more significant than nano-ZnO. P25 is significant for oxidative stress, antioxidant enzyme, and lipid peroxidation. P25 * nano-ZnO is the only significant interaction of pollutants, affecting macromolecules, lipid peroxidation, and photosynthesis activity. High-order interactions play significant roles in affecting multiple molecular components. Two groups of endpoints are best to reflect alga responses to interactively effects from P25, nano-ZnO, and triclosan. One is ROS, chlorophyll pigments, TBARS, area, MTT, and MMP, and the other one is chlorophyll pigments, ROS, TBARS, CAT, MTT and SOD. Our findings can be instructive for a comprehensive comparison among interactions of multiple pollutants and environmental factors in natural waters, such that more robust environmental toxicity analyses can be performed.