Four quantitative structure-activity relationships were developed for toxicity of selected photosynthesis (PHS) inhibitors and acetolactate synthase (ALS) inhibitors to Chlorella Vulgaris and Raphidocelis subcapitata using a mechanism-based approach. These models have good fitness and predictive ability. The potential of electron transfer, intermolecular interactions with weak electron-transfer, and intermolecular dispersive interactions between PHS inhibitors and the active site of action are key factors influencing the toxicity of these PHS inhibitors. Intermolecular weak electron-transfer interactions and intermolecular dispersive interactions mainly determine the toxicity of these ALS inhibitors. Sulfonyl is an important functional group governing the toxicity of ALS inhibitors investigated.