The production of reactive oxygen species (ROS) in plants under low temperature stress causes damage to plants. In order to evaluate the antioxidant responses of Thomson navel young trees (two years old) on different rootstocks under low temperatures, an experiment was conducted in a factorial plan based on completely randomized design. Treatments of temperatures were at seven levels including 9, 6, 3, 0, -3, $-6^{circ}C$, and $25{pm}2^{circ}C$ (as control) and rootstocks were Sour orange, Citrange and Trifoliate orange. Results of interactive effects of factors showed that electrolyte leakage (EL), antioxidant capacity, catalase (CAT) and ascorbate peroxidase (APX) activity were significant at P < 0.01. Maximum EL was observed in Thomson navel on Sour orange at $-6^{circ}C$, while the highest antioxidant capacity, CAT and APX activity respectively with mean 75.06%, 0.45 and $4.350IU{cdot}g^{-1};FW$ were observed in Thomson navel on Trifoliate orange rootstock at 0, -3 and $0^{circ}C$. Low temperatures increased EL, lipid peroxidation, antioxidant capacity, superoxide dismutase (SOD), APX, CAT and peroxidase enzyme activities (P < 0.01). Due to effects of rootstock, lipid peroxidation reduced to 52 % (P < 0.01). The biochemical and physiological study of this experiment indicated that Thomson navel on Trifoliate orange rootstock, had best tolerance to freezing stress.