In order to solve the challenge of digital engineering quality comprehensive control analysis, in view of the shortcomings of the existing divide and conquer algorithms, this study introduces an innovative engineering quality comprehensive control analysis method based on cluster analysis. This new scheme uses the principles of iterative product theory to accurately identify and locate key influencing factors, and accordingly makes a wise classification of indicators to reduce possible interference. At the same time, using the unique mechanism of cluster analysis, this scheme cleverly constructs a design strategy for comprehensive quality control. The empirical results show that the scheme shows a significant improvement compared with the traditional divide and conquer algorithm in terms of the accuracy of the comprehensive control and analysis of engineering quality, the processing efficiency of key factors and other key performance indicators, showing its obvious strong advantages. In digital engineering, comprehensive engineering quality control analysis plays a crucial role, which can accurately predict and optimize the growth trend and output results of digital engineering quality comprehensive control analysis. However, in the face of complex simulation tasks, traditional divide-and-conquer algorithms show some inherent shortcomings, especially when dealing with multi-level challenges, their performance is often unsatisfactory. To overcome this problem, this study introduces a new idea of comprehensive management and control analysis of engineering quality optimized by cluster analysis method, and accurately controls the influencing parameters through iterative product theory, and uses it as a road map for index allocation, and then uses cluster analysis method to innovate and construct a system scheme. The test results clearly point out that in the context of the evaluation criteria, the new scheme has been significantly optimized in terms of accuracy and processing speed for a variety of challenges, showing stronger performance superiority. Therefore, in the process of comprehensive control and analysis of digital engineering quality, the simulation scheme based on cluster analysis method successfully overcomes the shortcomings of the traditional divide and conquer algorithm, and significantly improves the accuracy and operation efficiency of the simulation.