Nonlinear dynamics plays a crucial role particularly in equipment validation of preparation production, validation results of which will significantly influence the results and period of drug registration in drug production processes. In this research, the flow field and temperature field simulation, calculation and analysis are creatively carried out in terms of depyrogenation tunnel, a very popular preparation drying-sterilization equipment in pharmaceutical processes with strong dynamic characteristics. After construction of 3D model of this equipment using Catia and mesh generation applying ANSYS, the computational fluid dynamic (CFD) method and verification of irrelevance method are carried out regarding 6.05 million of meshes to identify the flow velocity model and heat transfer model inside the equipment, to further provide methodology for pharmaceutical process validation and to further optimize the design of control methods. After calculation and simulation, the low-velocity vortices of different sizes inside the hood and the drying chamber are identified, which could cause vials to fall down; meanwhile, vials that are farther away from the outlet receives less heat exchange effect, which would shrink the effective sterilization area, indicating an inadequate validation methodology in pharmaceutical processes