【Objective】 Grafting, as an ancient horticulture technology, can prevent soil borne diseases effectively during watermelon planting. Studies in the past demonstrated close relationships between soil-borne diseases and microbiota, but it is still unknown how rhizospheric microbial activity is affected by rootstock-scion interaction. The objective of the present study is to elucidate effects of rootstock-scion interaction on microbial activity in the rhizosphere of watermelon grafted on gourd in a variety of soils. 【Method】 Four types of soils were collected including black soil (from Jilin), red soil (from Hainan), yellow-brown soil (from Jiangsu) and desert grey soil (from Xinjiang) and four types of seedlings (bottle gourd, watermelon, watermelon grafted on bottle gourd rootstock and bottle gourd grafted on watermelon rootstock) were planted in the four types of soils, separately. Rhizosphere soils were collected after 45 days. The BIOLOG method was used to explore differences between the treatments of the experiment in soil microbial activity. 【Result】Two-way PERMANOVA (Permutational multivariate analysis of variance) showed that soil microbial activity varied remarkably with soil type (R²= 0.534, p<0.001), and significant differences were observed in utilization of microbial carbon sources between grafted plants, i.e. grafted watermelon and grafted gourd (R²= 0.075, p<0.001). The treatment of watermelon was the highest in comprehensive utilization level of carbon source by rhizospheric microbiota, and followed by the treatment of grafted bottle gourd, the treatment of grafted watermelon, and the treatment of bottle gourd in the end. Principal component analysis (PCA) also showed that rootstock-scion interaction had an influence on microbial carbon sources utilization in different soil types. Heatmap analysis further demonstrated that grafting varied the microbial utilization of 31 sole carbon sources. For instance, the microorganisms in own-root bottle gourd rhizosphere utilized less carbohydrates, amino acids, polymers, phenols and amines compared to own-root watermelon and grafted plants, whereas they utilized more carboxylic acids such as γ-hydroxybutyric acid and α-keto butyric acid. On the contrary, the microbiome in own-root watermelon rhizosphere preferred to metabolize more carbohydrates, amino acids, polymers, phenols and amines, but less carboxylic acids. Compared with own-root watermelon treatment, grafted watermelon showed a lower absorbance level of various carbon sources such as carbohydrates, amino acids, which suggested that rootstock-scion interaction changed microbial metabolic pattern in rhizosphere. Aggregated boosted tree analysis (ABT) proved that soil available nutrients (such as readily available potassium and readily available phosphorus) were main influencing factors of carbon utilization by microbiota. 【Conclusion】 Both soil types and plant types can affect microbial activity in rhizosphere. Rootstock-scion interaction varied microbial metabolic pattern significantly. This study evaluated responses of microbial activity in rhizosphere to rootstock scion interaction in different types of soils, with results which may serve as theoretical basis for control of soil-borne diseases.