The article is devoted to the current problem of optimizing transport flows implemented within a mechanical engineering enterprise, where the efficiency of logistics operations directly affects the productivity and competitiveness of production. Optimization of the parameters of transport flows implemented within a mechanical engineering enterprise is a crucial component of technical production planning. The paper presents the results of the cargo transportation process analysis, defining many of its structural elements. Using these structural components, a multi-level model for designing and comprehensive optimization of transport flows has been developed. A two-level model of comprehensive structural and parametric optimization of individual transport operations has been proposed. A multi-level system of indicators for assessing the effectiveness of individual transport operations and transport routes has been developed. The article presents the results of testing the proposed model. During the study, a structural analysis of transport flows at a mechanical engineering enterprise was conducted, and a system for their comprehensive optimization was developed. The key element of the system was a modular algorithm for designing transport operations, ensuring flexible planning taking into account actual production constraints. The use of a robust approach and vector optimization criteria made it possible to develop solutions that are robust to uncertainties: a reduction in the target indicator of uniformity of labor intensity distribution by 22.5% and in the indicator of uniformity of cargo weight distribution by 17.33% was achieved. Moreover, the efficiency coefficient of vehicle utilization in terms of carrying capacity increased by 21.67%, and the actual values of the target indicators exceeded the optimization ones by an average of 6.4% and 2.72%, respectively, which confirmed the operability and stability margin of the solutions. The practical significance of the approach lies in the possibility of autonomous use of the system or its integration into the general production management system. The implementation of the subsystem will improve the rhythm of transport operations, reduce downtime, and minimize the risk of disruptions to production cycles.