Aiming at the flexible manufacturing system with multi-machining and multi-assembly equipment, a new scheduling algorithm is proposed to decompose the assembly structure of the products, thus obtaining simple scheduling problems and forming the cOrrespOnding agents. Then, the importance and the restriction of each agent are cOnsidered, to obtain an order of simple scheduling problems based on the cooperation game theory. With this order, the scheduling of sub-questions is implemented in term of rules, and the almost optimal scheduling results for meeting the restriction can be obtained. Experimental results verify the effectiveness of the proposed scheduling algorithm.