Because of its relatively long lifetime among short-lived climate forcers in the atmosphere, carbon monoxide (CO) is utilized as a tracer, and is expected to be simulated at coarse resolution. To better grasp the behavior of CO in the atmosphere, multi-altitude measurement is required because the main sources of CO emissions are automobiles (surface) and industry (aloft). In this work, using CO measurements obtained at remote sites and through a tower measurement network in Japan (37 m and 250 m above ground level (AGL) in an urban area, and 32 m AGL at a rural site in the greater Tokyo area), the performances of a global model (2° × 2.5°) and a regional model at various resolutions (12, 4, and 1.3 km) were comprehensively evaluated. The global model successfully simulated CO at remote sites but not for high-concentration peaks at rural and urban sites, whereas the regional model increasingly improved its performance in capturing CO peaks at urban sites with resolutions up to 4 km. Therefore, we concluded that a 4 km resolution was suitable for capturing CO at urban sites, and furthermore estimated the source contributions. The regions surrounding the greater Tokyo area were dominated by the concentration from the lateral boundaries (approximately 180 ppbv), while the higher CO in central Tokyo was attributed to local sources. These local sources accounted for up to 80% of the annual average at the surface level and just 10% aloft (corresponding to the 250 m AGL site). Sensitivity simulations assessing CO sources (automobiles, industry, and others) demonstrated the important role of automobiles, while higher altitudes had more sources attributed to industry. Local sources were found to make more prominent contributions at higher concentration ranges. The appropriate modeling resolution for CO behavior can be drawn from our findings and the usefulness of simultaneous measurements at the surface level and using a tower for capturing the three-dimensional CO structure can be demonstrated as an important approach.