The overall performance analysis model of an aircraft engine is an important tool for estimating engine performance. Traditional zero-dimensional models often fail to fully account for factors influencing the performance of engine components during the modeling process, which leads to cases where the component characteristic maps do not accurately reflect the real operating conditions of the engine components. In this paper, an overall performance analysis model considering design uncertainty is established. The main design uncertainty factors affecting engine component performance are selected and analyzed, including the impact of variable guide vane (VGV) settings on fan/compressor performance, the effect of tip clearance on compressor and high-pressure turbine (HPT) performance, and the influence of cooling air distribution on HPT performance. Meanwhile, the modeling method for considering design uncertainty factors in the zero-dimensional model is proposed. The overall performance analysis model of the engine, considering the above influencing factors, improves the level of model refinement and has significant application potential in practical engineering.