Safety is essential in human-robot collaborative assembly (HRCA), as humans and robots share close working spaces. Traditional safety assessment methods struggle to address the complexities of HRCA, often leading to non-implementation. Our model-based safety control system leverages Colored Petri Nets to reflect the needed flexibility, treating assembly steps as hazardous situations to evaluate task-based risk levels. The system features a modular design with separate human and robot subsystems, enabling a comprehensive risk assessment. Simulated evaluations of an industrial use case highlight the system’s capability to map the entire risk space, accommodate individual requirement restrictions, and assess mitigation strategies effectively.