Vertical thermal stratification is typical for partially conditioned large space building. Heat accumulation in the upper part of unoccupied zone will have significant effect on the cooling load of occupied zone. In order to accurately estimate this cooling load, calculation of the heat migration occurs in the thermally stratified environment is critical. Heat migration in this study refers to the amount of heat transferred from unoccupied zone to occupied zone (or between other adjacent zones). This paper discusses the method to calculate heat migration through convection and conduction in a large space building served by side wall nozzle air-supply system. In a scaled laboratory, three experiment cases with different exhaust air flow ratio are investigated. CFD simulations of the same cases are performed. Vertical temperature distribution and detailed cooling load results of the whole system as well as those of occupied zone are validated against experiment result. A detailed analysis on the total heat migration and its components between different zones is conducted. Inter-zonal heat transfer coefficient C_b used in a zonal BLOCK model and heat conductivity across the intersection of zones is obtained by dividing the whole space into two and four zones vertically. It is found that both C_b and thermal conductivity value across the intersection is greater than expected and affected by the local turbulent intensity.