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Dimensional quality is one of the most critical challenges in industries, which uses the multistage manufacturing process (MMP) such as assembly and machining for automotive and aerospace industries. According to investigations, fixture faults accounted for 72% of all the dimensional faults. Previous studies focused on only one fault or multiple faults occurred in one station or one fault in multiple stations, but these cases rarely appear in the real manufacturing. This paper presents a method for diagnosis of multiple fixture faults in the multi-station manufacturing process. The proposed method is based on the state space model of the MMP processes, which carries the information of the fixture layout geometry and sensor position. To identify the root cause, three continuous steps were used: a) development of the state space model and the construction of the statistics variables on offline mode, b) measurement of the coordinate measuring machines data on online mode and calculation of the statistics variables, and c) diagnostic algorithm for identifying the root cause. The presented paper integrates the state space model of the manufacturing processes and hypothesis test considering the impact of the measure noises. A case study verifies the proposed method.