This paper presents a novel modeling approach of coupling transient computational fluid dynamics (CFD) simulation with system identification for control system involving fluid flow and heat transfer. In order to illuminate the feasibility of this method, a fluid flow and heat transfer related process, i.e. a three dimension (3-D) spatio-temporal air temperature distribution and input (inlet air temperature) dependent process in the desert climate chamber, is considered. The distributed parameter models of the chamber temperature are identified using transient CFD simulation results and are then validated against the results obtained from the CFD simulations with high RT 2 (more than 0.97) and negative Young’s information criterion (YIC, less than −11.8). The PI controllers embedded in CFD simulation are then developed based on the models. The performance of the closed-loop systems is also evaluated within the full-scale CFD model. The results show that CFD-based system identification is feasible to model fluid flow and heat transfer related processes.