This study investigated the effects of grafting on eggplant growth, yield, and disease resistance, with a focus on microbial dynamics in the rhizosphere. Eggplant scions were grafted onto rootstocks of wild eggplant and tomato, with self-rooted eggplants serving as controls. Greenhouse experiments were conducted over an eight-month growing period, using standard field practices such as film mulching and integrated water–fertilizer management. High-throughput sequencing was used to analyze the biological properties and microbial community of the rhizosphere soil. Results showed that plants grafted onto ‘Huimei Zhenba’ and ‘Torvum’ rootstocks yielded up to 36.89% more than self-rooted controls, achieving yields of 4619.59 kg and 4399.73 kg per 667 m², respectively. The disease incidence of bacterial wilt was reduced to as low as 3.33% in the ‘Huimei Zhenba’ treatment, compared to 55.56% in non-grafted controls. Additionally, grafted plants exhibited increased stem diameter and chlorophyll content, with the TL/HM combination reaching 54.23 ± 3.17 SPAD units. The enhanced microbial biomass of carbon, nitrogen, and phosphorus, particularly in the TL/HM treatment (377.59 mg/kg, 28.31 mg/kg, and 36.30 mg/kg, respectively), supports a more nutrient-rich rhizosphere environment. Moreover, soil enzyme activities, such as β-glucosidase and phosphatase, were significantly higher in grafted plants, enhancing nutrient cycling and potentially increasing resistance to pathogens. Overall, grafted eggplants demonstrated enhanced soil microbial biomass, enzyme activity, and a more diverse microbial community, which are critical factors contributing to the improved yield and disease resistance observed in grafted crops.