Deep-seeding is an important cultivation way to absorb soil water in arid and semi-arid areas of our country. In this study, we analyzed the physiological and morphological phenotypic characteristics with a deep-seeding tolerant maize germplasm CGJ and a commonly used control Zheng58 as materials under treatments of normal 2 cm-sowing and 20 cm-sowing depth, respectively. The results showed that the main phenotypic characteristic of CGJ was the elongation of sprout mesocotyl under deep-seeding treatment, with a length of 10.68 cm, which was 2.5 times longer than Zheng58. The results of electron microscopy showed that the cells in CGJ mesocotyl were significantly stretched, that was 14 μm longer than Zheng58. CGJ had an earlier germination stage compared with Zheng58. The auxin content in CGJ mesocotyl was increased by 47.72 ng/mL. This result provided phenotypic and physiological information for breeding of deep-seeding tolerant maize.