Research on integrated process planning and scheduling (IPPS) is of great significance to the improvement of the overall quality of machinery manufacturing system. In the actual manufacturing process, the manufacturing system is often accompanied by some unpredictable uncertain disturbance factors, for instance uncertain processing time of jobs and changes of due date, etc. These uncertain disturbance events will ultimately affect production efficiency and customer satisfaction. Consequently, this paper considers the multi-objective IPPS problem with uncertain processing time and uncertain due date. A multi-layer collaborative optimization (MLCO) method is designed for the fuzzy multi-objective IPPS (FMOIPPS) problem, including three layers. For the process planning layer, the basic genetic algorithm is used to provide various near optimal process plans for the process selection system. For the process selection layer, a multi-objective genetic algorithm (MOGA) is designed to optimize the process selection population. A sharing function method is introduced to maintain population diversity. An individual comprehensive evaluation method is introduced to evaluate non-dominated solutions. The crowded distance, fast non-dominated sorting and elite strategy based on NSGAII is adopted in the proposed MOGA. The external archive method is employed to preserve the non-dominated solutions generated during population evolution. For the scheduling layer, a MOGA with a boundary search strategy is proposed. The boundary search strategy is designed to improve the search ability of boundary solutions. Three optimization objectives are minimizing the spread of fuzzy makespan, minimizing fuzzy makespan and maximizing average customer satisfaction simultaneously. The target of scheduling layer is to make scheduling arrangements for the process information obtained by process selection layer. Through mutual cooperation among each layer, guide the overall optimization process, and finally get satisfactory solutions. Different problem examples of various scales are employed to verify feasibility and effectiveness of the MLCO method. The experimental results indicate that the MLCO method can effectively address FMOIPPS problem.