Intercropped systems are regarded as a promising strategy for generating multiple benefits to the ecosystems in the rubber-plantation zone. However, knowledge about the impacts of intercropped systems with rubber on carbon and nitrogen storage in soils and their affecting factors is limited. In this study, three rubber-based intercropped systems, including rubber intercropped with Theobroma cacao, Coffea liberica, and Camellia sinensis, as well as rubber monoculture, were selected in Xishuangbanna, a typical rubber plantation zone in China. We collected soil samples from 0–10, 10–20, and 20–40 cm depths to analyze soil bulk density (BD), soil organic carbon (SOC), soil total nitrogen (TN), pH, the ratio of carbon and nitrogen (C/N), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON). The results showed that rubber trees intercropped with C. liberica significantly increased the SOC and TN stocks of the 0–40 cm soil layer by 19.9% and 13.6%, respectively, compared to rubber monoculture. Soil properties usually had strong relationships with SOC and TN stocks. Our study demonstrated that rubber with the C. liberica intercropped system had greater potential for C and N sequestration in this tropical region.