Abstract: Chlorophenols (CPs) are widely present in surface water and groundwater environments. They are one of the persistent pollutants in the environment. CPs in the water environment have a high half-life and are easily absorbed and enriched by aquatic organisms, causing toxic effects and harming aquatic organisms. This article aims to quantitatively identify the aquatic toxicity effects of CPs, assess potential ecological risks, and anticipate using source modification as a means to reduce and replace its ecological risks. The homology modeling and molecular docking method coupled with the simple formula scoring method was used to quantify the comprehensive aquatic toxicity effect of CPs molecules, and based on this, a 3D-QSAR model of the comprehensive effects on aquatic organisms was completed; and then molecular dynamics simulation technology was used to complete the CPs simulation verification of cumulative effects. Coupling the multi-dimensional assessment of functionality, environmental friendliness, and food chain cumulative risk, this article screened out low aquatic toxicity CPs alternatives that are both functional and environmentally friendly. The results of this research can provide a new perspective for the toxic effects and ecological risk assessment of CPs molecules, and provide theoretical support for the development of technology for environmentally friendly modification of CPs molecules.