We use the GEOS-Chem chemistry-transport model (CTM) to interpret the processes controlling the spatial-temporal variations of CO in the troposphere over the tropical biomass burning regions observed by the Tropospheric Emission Spectrometer (TES) and the Microwave Limb Sounder (MLS). Comparisons of the satellite observations and GEOS-Chem simulations, as well as analysis of the model meteorology and of tagged CO simulations, provide a detailed understanding of the interplay of convection and large scale ascent, as well as long-range transport, on CO emissions and thus on the model CO distribution. Our analysis reveals flaws in aspects of tropical transport in the GEOS-4 and GEOS-5 meteorological fields, and in the isoprene emissions in the model, as well as successes. We extended our examination to a higher altitude and explored mechanisms for the spatial-temporal variation of CO ‘tape recorder’ pattern in the upper troposphere and lower stratosphere (UTLS) as observed in MLS data. Both model simulations and the MLS data show a transition from semi-annual variations in the UT to annual variations in the LS, induced by a combination of the CO signal at the tropopause and the annual cycle of the Brewer-Dobson circulation. We further derived vertical velocities from MLS CO “tape recorder” pattern and used them as an independent evaluation of the GEOSs fields in the UT region. The vertical velocities in GEOS-4 agree well with them between 215 hPa and 125 hPa in boreal summer, fall and winter, while the velocities in GEOS-5 are too low in all seasons.