Citrus fruits are one of the most important horticultural fruits in the world. Low-temperature stress, as one of the most important environmental stresses, prevents plant physiological processes causing yield decline or palnt death. In this research, the interaction of the amino acid proline at concentrations of 0, 15, 20 mM and putrescine at concentrations of 0, 5 and 10 mM at temperatures of 1, -1, and -3°C was studied to investigate the changes of antioxidant systems in fruits of three Citrus speices. Antioxidant activity were meatured using the reducing power (RP) method and the ABTS free radical scavenging methods. Further, phenolic compounds were studied by high-performance liquid chromatography (HPLC). Low temperature, proline and putrescine increased antioxidant activity. The HPLC chromatograms showed that with decreasing temperature, level of phenolic compounds, except naringin, increased. Exogenous pplication of proline and putrescine increased phenolic compounds contents including chlorogenic, gallic, p-coumaric, and ferulic acid from phenolic acids and quercetin and rutin from flavonoids. The amount of tannic and salicylic acid was negligible. The highest and lowest levels of antioxidant capacity in treated and untreated fruits were observed in C. reticulata and C. paradisi respectively, indicating that C. reticulata has a higher resistance than the other species. The highest amount of antioxidants was observed in fruits treated with 20 mM proline. It is concluded that application of proline and putrescine under low temperature stress leads to improving the resistance of Citrus species by regulating and increasing antioxidants activity as well as increasing phenolic compounds and flavonoids.