As an organochlorine pesticide, methoxychlor (MXC) has been widely used in agriculture, resulting in a high frequency of detection in both the aquatic and sediment environment, and has toxic effects on aquatic species. Therefore, it is critical and necessary to derive Chinese MXC water quality criteria (WQC) and sediment quality criteria (SQC), and perform the ecological risk assessment for protecting aquatic organisms. The acute toxicity data of 17 aquatic organisms and the chronic toxicity data of 10 aquatic organisms were obtained through collection and screening. The best fit of the species sensitivity distribution (SSD) model was selected to derive the WQC, the short-term WQC (SWQC) and long-term WQC (LWQC) of MXC for aquatic organisms were 0.75 μg/L and 0.11 μg/L, respectively. Furthermore, the SQC was derived based on WQC by using the phase-equilibrium partitioning method. The resulting SQC-low (SQC-L) and SQC-high (SQC-H) were 0.73 mg/kg and 0.11 mg/kg, respectively. Moreover, the exposure concentration data of MXC in surface waters and sediments were collected, the ecological risk was evaluated by using risk quotients (RQ) method. The result showed that there were certain MXC ecological risk in surface water and sediments. The work will provide a valuable reference for protecting aquatic organisms and minimizing MXC ecological risk in China.