Large space buildings play a significant role in modern society because of their environmental advantages and market value. While the zonal model is promising for the efficient and rapid evaluation of the stratified thermal environment, there is a lack of a reasonable and convenient zoning strategy with the advent of modern computing. This paper presents a universal and practical zonal model, in which a simplified momentum equation is applied to consider air momentum preservation, transformation, and dissipation. Hence, the zoning structure is generalized and flexible. Moreover, limiting the dimensionless temperature constraint between adjacent zones establishes the connection between thermal nonuniformity and zoning results automatically. Simultaneously, the dimension and number of zones should be restricted within reasonable ranges to satisfy the characteristics of zonal simulation and reach the criteria of convergence. To further explore and validate the zonal model, a reduced-scale experimental model was constructed to replicate the thermal stratification in a mechanically ventilated large space by considering many crucial realistic factors. A particle image velocimetry (PIV) measurement was then conducted to visualize the airflow pattern and support the partition of zones. The results showed that the zonal simulation with adaptive zoning method can realize a similar accuracy with fewer zones and exhibit a better tolerance for zoning results compared to the conventional empirical zoning method. Furthermore, a case study of an atrium was performed to demonstrate the practicality and efficiency of the method for long-term dynamic simulations of complex thermal environments and building energy use.