The objective of the present study was to investigate the residue depletion of EF and CF in yellow catfish to estimate its WTs in plasma and tissues after multiple oral doses for 3 days at 20 mg/kg at 15, 20, and 25 °C. Samples were collected at pre-designed time points after oral doses. A validated method was performed to quantify EF and CF in plasma and tissues by high-performance liquid chromatography. Statistical differences were conducted using one-way ANOVA analysis. According to the maximum residue limit of China and Europe considering 95% percentile with 95% confidence, the WTs were estimated to be 44, 72, 66, 99, and 95 days at 15 °C; 32, 66, 65, 86, and 73 days at 20 °C; and 32, 61, 64, 55, and 59 days at 25 °C in the plasma, muscle and skin, gill, liver, and kidney, respectively. We found that increased temperature shortened the WTs in plasma and tissues. Therefore, this study can help the risk assessment of EF in aquatic products for human health at different temperatures to avoid residue violation.