Complex systems’ modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of various data and knowledge sources, models of various kinds (data‐driven models, numerical models, simulation models, etc.), and intelligent components in one composite solution. Growing complexity of such composite model leads to the need of specific approaches for management of such model. This need extends where the model itself becomes a complex system. One of the important aspects of complex model management is dealing with the uncertainty of various kinds (context, parametric, structural, and input/output) to control the model. In the situation where a system being modeled, or modeling requirements change over time, specific methods and tools are needed to make modeling and application procedures (metamodeling operations) in an automatic manner. To support automatic building and management of complex models we propose a general evolutionary computation approach which enables managing of complexity and uncertainty of various kinds. The approach is based on an evolutionary investigation of model phase space to identify the best model’s structure and parameters. Examples of different areas (healthcare, hydrometeorology, and social network analysis) were elaborated with the proposed approach and solutions.