Salicylic acid (SA) can induce multiple stress tolerance in plants. This study investigated the relationship between SA and antioxidant enzyme activities in maize seedlings under chilling stress. Changes of endogenous SA, antioxidant enzyme activities and malondialdehyde (MDA) concentrations were assessed in two different chilling-tolerant maize inbred lines (Huang C and Mo17) under chilling stress. The results showed that both endogenous free and bound salicylic acid contents increased in roots and leaves of both lines. MDA concentrations also increased significantly in roots and leaves of both lines after chilling stress. In addition, in Huang C, chilling stress increased the activities of four antioxidant enzymes, ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR) and peroxidase, while in Mo17, only CAT and APX increased. Furthermore, a regression analysis was conducted between SA and MDA concentrations or antioxidant enzyme activities under chilling stress. The results indicated that MDA concentrations were positively correlated with total SA contents in roots (r = 0.9776, p = 0.0224) and bound SA in leaves (r = 0.9974, p = 0.0458), respectively. Total SA contents had positive correlations with APX activities both in roots (r = 0.9993, p = 0.002) and leaves (r = 0.9630, p = 0.037) and GR in leaves (r = 0.9298, p = 0.0221). Together, these results suggested that chilling stress improved the biosynthesis of endogenous SA, and lipid peroxidation and antioxidant enzyme activities could be indicated by endogenous SA contents of maize seedlings under chilling stress. Furthermore, increased activities of antioxidant enzymes, especially in roots, may contribute to the chilling tolerance of maize seedlings.