The air supply terminal located at the floor level attached to side-wall is widely used in large space buildings, leading to potential energy saving as well as significant vertical thermal stratification. The cooling load calculation of such system is challenging, especially the calculation of the load gained from unoccupied zone. This paper adopts experiment and computational fluid dynamics (CFD) methods to study the heat transfer upward and downward across the stratified surface in large space building with floor-level side wall air-supply system. Five experimental cases with different heat source power and exhaust airflow ratios are performed to study their effects on the indoor thermal environment. We investigate the same cases in CFD and verify the result of vertical temperature distribution and cooling load components. As a critical parameter in evaluating the thermal stratification environment of large space building, the inter-zonal heat transfer coefficient Cb is emphatically discussed. By comparing the Cb value obtained through the two methods, the accuracy of the microscopic method is verified by the heat balance method. The results show that the Cb value is mainly affected by the zonal division and air distribution, but less prominently by exhaust airflow ratio and heat source in the occupied zone.