The fluctuation of various parameters in the production process increases the risk of generating unqualified products and suffering from systematic failures and downtimes, and the preventive maintenance and control of potentially faulty machines in manufacturing systems should consider the continuous increase of operational risk. Therefore, to proactive control the manufacturing system operational risk, a joint model of risk-based maintenance (RBM) and integrated monitoring is proposed. The proposed model formulates an appropriate maintenance strategy and appropriate control charts for monitoring the manufacturing process, guaranteeing the stable operation of the manufacturing system. First, considering the co-effect of the production equipment state and workpiece quality, a novel connotation of the manufacturing system mechanism’s operational risk is proposed, and the RBM framework is constructed. Second, considering the manufacturing system operational state, an integrated maintenance decision-making model based on different risk scenarios is established using a dynamic monitoring scheme based on EWMA control charts. Third, a particle swarm optimisation algorithm is adopted to optimise the proposed model to obtain the optimal maintenance strategy for production equipment and monitoring parameter for workpiece quality. Finally, the effectiveness of the proposed approach is illustrated with a case study on a subway current receiver production line.