Remanufacturing has been considered to be one of the most effective ways to deal with sustainable manufacturing. The integration of intelligent technology and remanufacturing assembly system is a necessary way for the development of remanufacturing industry. This paper proposes an intelligent control system for improving the quality and production efficiency of the remanufacturing assembly (reassembly) systems. First, the state space model of reassembly is constructed and deduced to reveal the quality transfer and coupling mechanism of reassembly process. An optimization model of the reassembly scheme is established for minimizing the comprehensive cost. Then, an intelligent control system for reassembly process is proposed, which is a real-time monitoring and dynamic compensation response to address abnormal quality and to achieve intelligent control of reassembly process. The data model, information perception and fusion technology, real-time monitoring and dynamic compensation of reassembly quality are studied and implemented. Finally, the prototype intelligent control system of reassembly is developed, which illustrates its practicability offering a technical support for sustainability of remanufacturing. It can monitor the abnormal quality in real time and make dynamic compensation response, and realize the intelligent control of reassembly process. It plays a positive role in improving quality, reducing cost and enhancing customer satisfaction. This intelligent control method is more suitable for the reassembly system of complex machinery, especially under uncertain operating environment.