Rubber-based agroforestry (Hevea brasiliensis) systems are considered the best way to improve soil properties and the overall environmental quality of rubber monoculture, but few reports have examined soil aggregate stability in such systems. The objective of this study was to examine the management and landscape effects on water stable soil aggregates, soil aggregate-associated carbon, nitrogen content and soil carbon, and nitrogen accumulation in Xishuangbanna, southwestern China. Treatments were rubber monoculture (Rm) and four rubber-based agroforestry systems: H. brasiliensis–C. arabica (CAAs), H. brasiliensis–T. cacao (TCAs), H. brasiliensis–F. macrophylla (FMAs) and H. brasiliensis–D. cochinchinensis (DCAs). The results showed that, with the exception of CAAs, the rubber-based agroforestry treatments significantly increased total soil organic carbon (SOC) and N contents and enhanced the formation of macroaggregates compared to the rubber monoculture treatment. SOC and N contents in all water-stable aggregate fractions were significantly higher in rubber-based agroforestry systems (except CAAs) compared to rubber monoculture. The macroaggregate fractions contained more organic carbon and nitrogen than the microaggregate fractions. The proportions of C and N loss from slaking and sieving were shown to have significantly negative correlations with the mean weight diameter and the SOC and N concentrations in bulk soil. The results suggest that soil surface cover with constant leaf litter fall and extensive root systems in the rubber-based agroforestry systems increased soil organic carbon and nitrogen, helped improve soil aggregation, reduced soil erosion, decreased carbon and nitrogen loss, and ultimately improved the carbon and nitrogen accumulation rates. Given that the soil physical-chemical properties improvement and the patterns of the intercropping system played key roles in managing artificial forests, we recommend that local governments and farmers should prefer T. cacao, F. macrophylla and D. cochinchinensis and not C. arabica as the alternative interplanted tree species within rubber plantations.