In order to solve the problems of process quality evaluation in the discrete manufacturing of RF and microwave products under the multi-type and variable batch mixed production mode, a comprehensive evaluation method of process quality level was proposed. Based on the clustering of production process quality data, the process quality evaluation framework and the bottleneck degree evaluation algorithm were constructed by combining the analytic hierarchy process (AHP), and the properties of the model and the algorithm under various constraints such as different varieties, batch and mixed-line discrete manufacturing modes were discussed. Taking the micro-assembly process quality data of microwave and radio frequency products as an example, the evaluation method was verified. The results show that the evaluation model has a good ability to evaluate the process quality.