A water environment can impact many physiological processes of aquatic animals. The antioxidant response of immune system of the pearl oyster to temperature and salinity is of great significance to health. This study analyzed the physiological changes and immune responses under different temperature and salinity levels (temperature: 20, 25, and 30 °C; salinity: 23, 28, and 33‰) in the short term (7 d) in the hepatopancreas and other tissues of 405 pearl oysters. The combined effects of temperature and salinity on antioxidants in the immune system of the pearl oyster were evaluated via response surface methodology and Box–Benhnken design (BBD) under laboratory conditions. The secondary effects of salinity on the activities of glutathione peroxidase (GSH-PX), catalase (CAT), and superoxide dismutase (SOD) were significant, and CAT and SOD showed an inverted U-shaped trend with the increase in salinity. Temperature significantly impacted GSH-PX, CAT, glutathione (GSH), and SOD in primary and secondary effects, and the maximum values of CAT, GSH, and SOD were observed. The phenoloxidase (POX) and alkaline phosphatase (AKP) activities increased with the increasing temperatures. The interaction of temperature and salinity was significant on CAT and SOD, but was not significant on GSH-PX. The interaction between salinity and temperature on AKP was significant, which was contrary to the results of AKP in the hemolymph. The expression levels of antioxidant genes varied between tissues, and the expression levels of different genes in the same tissue were different. Appropriate immunity and antioxidant index models were established under the combined temperature and salinity conditions. The optimal combination of temperature and salinity was 24.95 °C and 28.11‰, respectively, and the desirability was 0.803. This study provides theoretical reference points for the pearl oyster to respond to temperature and salinity changes and can be used to establish an index model for shellfish aquaculture.