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Water pollution is an increasingly serious problem. Here, Cu and Zn ions were used as stress factors, and G. affinis served as a test organism. Fluorescence quantitative PCR was used to detect changes in the expression of antioxidant genes (SOD, GST, CAT), heat stress genes (Hsp70, Hsp90, Hspd1, Hsc70), and immune system-related genes (IL-1β, IL-8) in G. affinis exposed to Cu and Zn ions over time. To explore the toxic effects of Cu and Zn on G. affinis. The results showed that the 48 h LC50 concentrations of the heavy metals Cu and Zn to G. affinis were 0.17 mg/L and 44.67 mg/L, respectively. Within 48 h, with prolonged Cu exposure, the relative expression levels of the Hsp70, Hsp90, Hspd1, Hsc70, SOD, GST, and CAT genes in the gill tissue first showed a significant increase and then gradually decreased. Gene expression peaked between 9 and 36 h. The relative expression levels of SOD and GST genes in liver tissue showed a gradual decline. Within 48 h, with prolonged Zn exposure, the expression levels of SOD, CAT, and GST genes in G. affinis first increased and then fell before finally rising. The expression levels of IL-1β and IL-8 mRNA showed varying degrees of upward trends, and the expression of IL-8 was the highest for all gill tissue. To sum up, Cu and Zn have strong toxic effects on G. affinis, which makes it possible to use G. affinis as indicator organisms for aquatic environmental pollution.