Flow distortion over a forested hill is asymmetric, forming a recirculation region on the lee slope that increases the complexity in understanding atmosphere–biosphere interaction. To understand the complexity, we examine the effect of the geometry of forested hills on recirculation formation, structure, and related CO2 transport by performing numerical simulations over double-forested hills. The ratio (0.8) of hill height (H) to half length (L) is a threshold value of flow patterns in the recirculation region: below 0.8, sporadic reversed flow occurs; at 0.8, one vortex is formed; and above 0.8, a pair of counter-rotating vortices is formed. The depth of recirculation increases with increasing H/L. The contribution of advection to the CO2 budget is non-negligible and topographic-dependent. Vertical advection is opposite in sign to horizontal advection but cannot exactly offset in magnitude. Height-integrated advection shows significant variation in fluxes across hills. Gentle slopes can cause larger advection error. However, the relative importance of advection to CO2 budget is slope-independent.