Per- and polyfluoroalkyl substances (PFASs), synthetic organofluorine compounds containing at least one fully fluorinated carbon unit (-CF₂- or -CF₃-), encompass both legacy PFASs and their structurally related substitutes. As emerging PFASs, their alternatives have been garnering significant attention; however, a systematic analysis of the potential risks they may pose, particularly to green algae photosynthesis in aquatic environments, remains lacking. This study selected 57 emerging and eight traditional PFASs molecules and nine characteristic proteins/enzymes related to green algae photosynthesis to construct a graded evaluation index of the interference effect of PFASs exposure on green algae photosynthesis. Through molecular docking and molecular dynamics simulations, the characterization values of interference effects were calculated, and five key pathways of the interference effect system were identified. Among all molecules, nine PFASs reached the special risk level, and 21 PFASs were identified at the key risk level. Extreme Gradient Boosting combined with Shapley Additive Explanations (XGBoost-SHAP) further identified that the chain length, electron-withdrawing ability, and oxidizability of PFASs were the dominant molecular features interfering with green algae photosynthesis. A priority control list of PFASs with interference effects was then developed and validated. This study systematically reveals the molecular interference mechanism and risk grading characteristics of emerging PFASs on green algae photosynthesis, elucidating their potential impact on aquatic ecosystem functions through the disruption of key photosynthetic processes. These findings provide theoretical support for the risk identification and management of emerging PFASs.