A three-dimensional physical-biogeochemical ocean numerical model with eddy-permitting horizontal resolution was applied to simulate upper-ocean carbon cycle variabilities in the Tropical Maritime Continent (TMC) over the last decade (2010–2019). Forced by atmospheric and oceanic reanalysis products with high temporal resolution, the model showed robust consistency with the observed seasonality of pCO2 and atmospheric CO2 sink/source characteristics across the modeling domain. Within the TMC, the model results indicated strong CO2 degassing along the west of Sumatra-south of Java associated with the seasonal cycle of the upwelling system in the area. While acting as a full-year atmospheric CO2 source, the TMC exhibited pronounced interannual modulation in both pCO2 and sea-air CO2 flux over the last decade. Large-scale anomalous strong CO2 degassing from 2015 to 2016 in response to the evolution of the 2015/2016 El Niño was observed from the simulation results. Modulations related to the Indian Ocean Dipole (IOD), on the other hand, were confined along the west of Sumatra-south of Java with a higher magnitude compared with anomalies related to El Niño/La Niña. Simulation results also captured the asymmetric response of the upper-ocean carbon cycle to the IOD over the last decade, where anomalies during negative IOD (nIOD) were notably strong despite being indicated as weak nIOD events by the Dipole Mode Index.