More and more public buildings have functional zones without physical partitioning, and non-uniform thermal environments often exist inside it. Understanding this phenomenon and its influences on HVAC energy consumption is of great significance. Field measurements were carried out on a transport station in Nanjing, South China during daytimes, and thermal stratifications were found to be evident in the non-air-conditioned atrium with the linear gradients being range of 0.06–2.0 °C/m. An energy model coupled with CFD model is developed and verified by measured data. Further simulations are performed under cases of atrium height, glazed-roof material and season. The results show that the CFD simulated convective heat transfer coefficients of inner surfaces (CHTCIS) of the atrium vary according to scenario; linear temperature gradients differ by cases, and specifically there are two gradients in hot summer with the dimensionless interface heights being approximately 0.56–0.6; the HVAC loads of the air-conditioned zones are estimated to be 115–146 W/m2 when adopting thermal stratification and user-defined CHTCIS, and larger than that when no thermal stratification and built-in CHTCIS. The double low-e 6 mm plane glass contributes to the most favorable temperatures in both cold winter and hot summer, followed by the smallest HVAC loads.