Modeling and simulation of human-centered systems is a tremendously challenging problem because of the increasing crucial roles of humans in complex systems due to uncertainty and non-deterministic nature of human actions. To aid in designing and developing a control scheme for complex semi-automated systems catering for humans, this research provides a modeling vision and presents an agent-based simulation framework for a human-involved system. With the deterministic nature of automated system control models, stochastic and non-deterministic traits of human decision making processes are considered within the proposed modeling framework. To demonstrate the model’s applicability, human-machine cooperative environment of a material handling example is illustrated. We envision that the proposed agent-based and human-machine collaborative simulation model can provide an effective framework to incorporate humans in designing and implementing complex and multi-scale system control environments