Abstract: Two different drought tolerance soybean (Glycine max) varieties (Nannong 99-6 and Kefeng 1) were used to study the effects of α-naphthaleneacetic acid (NAA) on the antioxidation system under longterm drought stress after flowering with pot experiment, which lasted for 110 days at Pailou Experiment Station, Nanjing Agricultural University, in 2012. The results showed that longterm stress decreased the shoot dry mass significantly, however, increased the level of reactive oxygen species (ROS) and malondialdehyde (MDA) content. It also obviously increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), glutathione reductase (GR) and glutathione peroxidase (GPX). The contents of ascorbic acid (AsA) and glutathione (GSH), and the ratios of AsA/DHA (dehydroascorbic acid) and GSH/GSSG (L-glutathione oxidized) were obviously enhanced. Kefeng 1 showed a higher antioxidation ability than Nannong 99-6, and could consequently maintain lower ROS and MDA levels. NAA distinctly enhanced the activities of APX, POD, CAT, MDHAR, GPX, and ratios of AsA/DHA and GSH/GSSG, while decreased the levels of ROS and MDA. The AsA content and dehydroascorbate reductase (DHAR) activity were significantly increased in Kefeng 1.