Complex engineering systems can be continuous, discrete, as well as hybrid. Comparing with other kinds of complex engineering systems, the hybrid one is the most difficult to be analyzed because of its combination of continuous and discrete behaviors of the system, as well as the internal and external uncertainties. It is necessary to model and simulate the complex engineering system to explore its dynamics and evaluate the effect of different management strategies. Existing modeling and simulation methods of complex engineering systems, especially hybrid system, mostly focus on solving problems in specific systems or scenarios, neglecting the reusability and simplicity of methods. In this paper, a universal hierarchical modeling method for complex engineering system is proposed, which illustrates how to deal with continuous and discrete dynamics, and hybrid simulation method is applied to verify the feasibility and availability. A copper smelter is taken as one case of complex engineering system, and the production process in the smelter is described by the proposed method. Results of simulation show that the universal hierarchical modeling method can describe complex dynamics in the system properly and simply, which contributes to the study on complex engineering system.