Onychostoma macrolepis has becoming an endangered fish species in China, which population gradually declined in the past few decades due to the changing environment including elevated water temperature resulted from adverse weather events. The present study determined antioxidant defenses of O. macrolepis in response to thermal stress, aiming to understand the role of antioxidant system in adaptation of thermal stress for O. macrolepis. Experimental fish which were acclimated at 24 °C were stressed at 30 °C for 0 h, 1 h, 3 h, 6 h, 12 h, 24 h and 48 h, respectively. Change in mRNA expression of Cu/Zn superoxide dismutase (Cu/Zn-SOD) and catalase (CAT) and activity of SOD and CAT of the experimental fish with different stress time were determined. We cloned the full-length cDNA of Cu/Zn-SOD and CAT by means of RACE method, and analyzed their molecular characterization and tissue distribution. We discovered that the mRNA expression of the Cu/Zn-SOD in heart, liver, spleen, gill, intestine and the CAT in heart, liver, spleen, kidney, intestine and muscle of O. macrolepis significantly increased when water temperature increased from 24 °C to 30 °C, indicating a sensitive response of mRNA expression of Cu/Zn-SOD and CAT to the thermal stress. Moreover, the mRNA expression of the Cu/Zn-SOD and CAT were varied in different tissues, indicating different sensitivity of the tissues in response to thermal stress. Activity of the SOD in serum of O. macrolepis gradually increased from 1 h to 12 h sampling time, but significantly decreased at 24 h sampling time, compared to that of 0 h sampling time. And activity of the CAT in serum of O. macrolepis significantly decreased from 1 h to 12 h sampling time, and did not changed significantly at 24 h and 48 h sampling time, compared to that of 0 h sampling time. As such, MDA contents in the serum of O. macrolepis significantly decreased from 1 h to 6 h sampling time, but significantly increased at 12 h and 24 h sampling time, compared to that of 0 h sampling time. In summary, antioxidant system of the O. macrolepis can quickly response to short term thermal stress at 30 °C in form of both the mRNA expression of Cu/Zn-SOD and CAT and the activity of SOD and CAT, and consequently enhance the antioxidant defenses of O. macrolepis. However, thermal stress at 30 °C for 12 h-24 h seems to lead to oxidative damage of the O. macrolepis.