Abstract: Schizothorax prenati, an important cold-water fish in China, is a precious commercial fish in the upper Yangtze River. The current study investigated the effects of heat stress and recovery on the damage of organism, the functions of non-specific immunity and apoptosis in Schizothorax prenati under 3 conditions:before heat stress (19℃, control group), after heat stress (27℃ for 0, 2, 4, 8 and 12h, respectively; experimental groups) and 6h after heat stress recovery (19℃ recovery group). The results indicated that the activity of superoxide dismutase (SOD) increased at 0, 4, 8 and 12h after stress, and it increased significantly at 0, 12h compared with the pre-stress (P<0.01). The activity of myeloperoxidase (MPO) reached the maximum level at 4h. The activity of glutamic-oxalacetic transaminase (GOT) in all experimental groups had no significant difference compared with the control group, and it was significantly higher than that in the control group at 6h after recovery (P<0.01). The activity of glutamic-pyruvic transaminase (GPT) at 0, 4, 12h after stress and 6h after recovery was significantly higher than that in the control group (P<0.01). The content of malonaldehyde (MDA) at 2, 4, and 12h after heat stress was significantly higher than that in the control group (P<0.01), and it was significantly higher than that in the pre-stress at 8h (P<0.05), which reached the maximum level at 12h after stress, and the content of MDA at 6h after recovery returned to pre-stress levels (P<0.05). C3 complement (C3) level kept rising and was significantly higher than that of the control group at 12h under heat stress (P<0.05), but it decreased at 6h after recovery having significant difference from the control group (P>0.05). Compared with the pre-stress group, apoptosis rate in all experimental groups was significantly higher after heat stress (27℃) (P<0.05) and reached the maximum level (52.42%) at 4h after treatment, while declined markedly at 6h after recovery. These results indicated that heat stress changed the non-specific immunity of the organism and induced inflammation and induced cells damage, but all functions can recover gradually after the temperature returning to the moderate level. The results provided basic data for further research on the mechanism of high temperature adaption in Schizothorax prenati, as well as a scientific basis for temperature control during cultivation and transit of this species.