Pesticides due to their extensive use have entered the soil and water environment through various pathways, causing great harm to the environment. Herbicides and insecticides are common pesticides with long-term biological toxicity and bioaccumulation, which can harm the human body. The concept of the adverse outcome pathway (AOP) involves systematically analyzing the response levels of chemical mixtures to health-related indicators at the molecular and cellular levels. The AOP correlates the structures of chemical pollutants, toxic molecular initiation events and adverse outcomes of biological toxicity, providing a new model for toxicity testing, prediction, and evaluation of pollutants. Therefore, typical pesticides including diquat (DIQ), cyanazine (CYA), dipterex (DIP), propoxur (PRO), and oxamyl (OXA) were selected as research objects to explore the combined toxicity of typical pesticides on Chlorella pyrenoidosa (C. pyrenoidosa) and their adverse outcome pathways (AOPs). The mixture systems of pesticides were designed by the direct equipartition ray (EquRay) method and uniform design ray (UD-Ray) method. The toxic effects of single pesticides and their mixtures were systematically investigated by the time-dependent microplate toxicity analysis (t-MTA) method. The interactions of their mixtures were analyzed by the concentration addition model (CA) and the deviation from the CA model (dCA). The toxicity data showed a good concentration–effect relationship; the toxicities of five pesticides were different and the order was CYA > DIQ > OXA > PRO > DIP. Binary, ternary and quaternary mixture systems exhibited antagonism, while quinary mixture systems exhibited an additive effect. The AOP of pesticides showed that an excessive accumulation of peroxide in green algae cells led to a decline in stress resistance, inhibition of the synthesis of chlorophyll and protein in algal cells, destruction of the cellular structure, and eventually led to algal cell death.