Rubber plantations represent 13 million hectares in the world. Many researchers have focused on the environmental sustainability of rubber plantations, with rubber-legume systems better approach for ameliorating soil environments. This study investigated the effect of introducing Flemingia macrophylla (a leguminous shrub) to different-aged rubber plantations on the emissions of CO2, N2O, and CH4. As trees aged in the rubber plantations, the annual emissions of CO2, N2O, and CH4 significantly decreased. The introduction of F. macrophylla to different-aged rubber plantations significantly decreased CO2 and CH4 flux but increased N2O flux. The CO2 and N2O fluxes were mainly affected by soil temperature at 10 cm depth, and CH4 flux was mainly affected by both soil water content in the 0–10 cm soil layer and soil temperature at 10 cm depth. Compared to the same-aged rubber plantations, annual total CO2 flux of young and mature rubber–F. macrophylla plantations decreased 154,000 and 64000 kg ha−1, CH4 flux decreased 0.50 and 0.78 kg ha−1 (17.0 and 26.5 kg CO2 eq ha−1), and N2O flux increased 0.15 and 0.55 kg ha−1 (44.7 and 163.9 kg CO2 eq ha−1), respectively. The rubber-leguminous shrub systems significantly improved soil organic carbon sequestration rate, relative to the same aged rubber plantations. In conclusion, the emissions of CO2, N2O and CH4 decreased as the trees aged in the rubber plantations, and rubber-leguminous shrub systems could mitigate local climate warming by reducing reduce greenhouse gas emissions and improving soil organic sequestration rate.