In view of the uncertainty in the quality evaluation for manufacturing process and multivariate process capability, a comprehensive evaluation approach is proposed by extending classic process capability index with considering variations of key quality characteristics among the whole manufacturing process, which includes the procurement, machining, assembling and delivery inspection processes. Meanwhile, to avoid the influence of uncertainties, the test, feedback and correction processes for the evaluation approach are added based on the Structure Equation Model (SEM). Then, after the evaluation result is calculated according to the evaluation approach, a method to monitor the deviations of the evaluation results is introduced based on the confidence interval. At last, the quality level of total manufacturing process is evaluated by combing the evaluation results and their confidence interval. Finally, a case study is carried out to verify the proposed method.