This study addresses the significant vertical temperature gradients (ΔT > 2.5°C/m), insufficient airflow throw distance, and airflow short-circuiting in large industrial workshops (height ≥10 m, span ≥30 m) for aerospace applications. Taking a 55 m and 115 m high vertical assembly and testing workshop for launch vehicles as the research object, this paper optimizes the airflow organization of the air conditioning system using Computational Fluid Dynamics (CFD) technology combined with PMV-PPD thermal comfort indices. A refined 3D model was established to analyze the effects of supply air angles, jet velocities, and return air layouts on temperature and velocity fields. The research results provide a scientific framework for the design of air conditioning systems in ultra-tall industrial spaces.