The objective of the study was to investigate the effect of water deficit during seedling stage on the structure of vascular bundles in different maize stems. Four maize varieties were grown in pots with two water treatments occurred at the seedling stage, including normal irrigation (75–80% of the field moisture capacity) and water deficit (4550% of the field moisture capacity). Vascular bundle area, xylem area and phloem area in the first internode of the basal stem decreased significantly and the vessel numbers and the vessel diameter were also in downward tendency compared with the contrast under water deficit. Since the area of single vascular bundle decreased, the numbers of vascular bundles within the unit visual field increased. Changes of vascular bundle structure in the ear internode to water deficit were similar to that of the first internode of the basal stem, however, the effect on vascular bundles became smaller and was mainly on the phloem area. Water deficit during the seedling stage increased the vascular bundle area, xylem area, phloem area, number of vessels and vessel diameter in the first internode of the ear stem. These results suggested that water deficit during the seedling stage had a long effect on the development of vascular bundles and a compensatory structural act was discovered in the late developed vascular bundles.