Sowing depth significantly affects ginger (Zingiber officinale Roscoe) yields, and sowing depth can affect rhizosphere community structure through root exudates. However, the relationship between the reaction process in root zone and ginger rhizome development is unclear. In this study, we investigated the rhizome and root development and rhizosphere environment at different sowing depths (2cm (SD2), 5cm (SD5), and 10cm (SD10)). It was found that SD10 significantly increased ginger yield, which is related to the development of vascular bundles and the expression of aquaporin. PLS-PM analysis found that root length, root absorption capacity, and soil enzymes have the strongest correlation with yield, while root diameter is negatively correlated with yield. Under SD10, the increase of auxin and ethylene content together with the expression of ARF7, LBD16, and PIN1 promoted the development of lateral roots. In addition, SD10 increased the secretion of root organic acids, amino acids, and carbohydrates, which in turn promoted the development of rhizosphere bacteria. The promotion of SD10 on nitrogen cycle and nitrogen fixation ability in turn promoted the development of ginger.