There has been a developing technology in algae with pharmaceuticals wastewater. However, the effect and the underlying mechanism of pharmaceuticals on algae are not well understood. To investigate the effect and mechanism of pharmaceuticalson microalgae, four pharmaceuticals of clofibric acid (CLF), ciprofloxacin (CIP), diclofenac (DCF) and carbamazepine (CBZ) on C. pyrenoidosa culture were analyzed. At low concentrations (<10 mg/L), the pharmaceuticals, especially the DCF, exhibited positive effects on both the structure and function of algal cultures; algal growth (i.e., chlorophyll a accumulation, lipid accumulation) and activities of antioxidant enzymes were stimulated. The algal metabolite differences of various DCF concentrations were investigated and a total of 91 substances were identified, whose samples were clustered and clearly separated. The key metabolomics pathway analysis found that the DCF promoted the carbohydrate and fatty acid metabolic pathway in C. pyrenoidosa under relatively low concentrations (<10 mg/L). However, the algae metabolomics pathway was disturbed significantly under the action of a high concentration of DCF (>100 mg/L). The study detected the effects of four pharmaceuticals on C. pyrenoidosa and demonstrated that the usage of metabolomics analysis complemented with DCF could be an effective approach to understand the mechanism of molecular evolution in C. pyrenoidosa for microalgal biomass and bioenergy from wastewater in researches of biological resources.