Water stress induces physiological changes in plants, and partial root-zone drying irrigation (PRD) is a water-saving irrigation strategy that can regulate plant physiological responses. This study was to investigate the physiological responses of maize and soybean to PRD and deficit irrigation (DI) under two N-fertilization levels. Plants were grown in a split-root pot culture and were exposed to three irrigation treatments, including full irrigation (FI), DI and PRD, at two fertilization levels (2 and 3 g Pot-1 N). We found that PRD and DI significantly decreased the biomass of two plant species and PRD inhibited less dry mass than DI. Water stress resulted in a higher leaf malondialdehyde content in the leaves of maize and soybean at two fertilization levels, with a smaller increment of PRD than DI. PRD had higher proline content in maize at high N fertilization and in soybean at normal N level than DI. Soluble sugar and protein contents of maize and soybean were higher under PRD than DI at two N levels, except soluble protein content of soybean at normal N level. PRD reduced superoxide dismutase, peroxidase and ascorbate peroxidase (APX) activities of maize and soybean. Moreover, soluble sugar content and APX activity of maize and soybean and proline and protein contents of maize were significantly affected by N treatments. These results indicate that PRD could alleviate the negative effects induced by water stress on maize and soybean through regulation of physiological parameters.