Moderate Resolution Imaging Spectroradiometer (MODIS) on Aqua has been in operation providing continuous global observations for science research and applications since 2002. The long-term stability of thermal emissive bands (TEBs) of Aqua MODIS was monitored through inter-comparisons with measurements by hyperspectral infrared sensors, such as AIRS on Aqua and IASI on MetOp satellite, or through long term vicarious monitoring over cold targets, such as Dome- C and deep convective clouds (DCC). In this paper, a radiative transfer modeling-based simulation model using Community Radiative Transfer Model (CRTM) is developed to perform the long-term monitoring of the stability of TEBs of Aqua MODIS. CRTM is a fast-radiative transfer model for calculations of radiances for satellite infrared radiometers and is able to output infrared radiance and brightness temperature at spectral bands of MODIS. Long term European Centre for Medium-Range Weather Forecasts (ECMWF) global atmospheric reanalysis data, such as temperature and humidity profiles, are used as inputs to the CRTM simulation. By confining the area of interest to be over low to middle latitude ocean, the long-term stabilities of selected Aqua MODIS TEBs are monitored through Observation–Background (O-B) brightness temperature (BT) bias between MODIS measurements and BT retrieval from CRTM simulation. The consistency and relative stability between Aqua MODIS and ECMWF reanalysis data for surface channels of MODIS are evaluated. In addition, the radiative transfer modeling with CRTM enables us to evaluate the impacts of long term variation of global CO2 distribution on the O-B BT biases for CO2 channels of Aqua MODIS through comparison of simulations with constant or long term variable CO2 as inputs. The O-B analysis with RTM show that Aqua MODIS surface channels are all radiometrically stable with yearly BT bias drift less than 0.004K/year for B20, B22, B23 and ~0.01K/year for B31 and B32. The CO2 absorption channels of Aqua MODIS, e.g. B33-B36, are stable with BT bias drift < 0.005K/year.