This paper focuses on the flexible packaging line for large length-to-diameter ratio heavy cylindrical products. It systematically analyzes the key bottleneck issues and proposes an optimized production line solution based on modular design. Based on the modular concept, the packaging process is decomposed into the loading module, inner packing processing module, packing module, sealing module, and stacking module. The functions of each module are clarified, and the connection sequence is optimized to achieve the compactness of the process flow and the efficient coordination of equipment. For the posture control, quality positioning, and safety protection requirements of single-root high-density materials during the packaging process, an “L-shaped + straight-line” layout scheme and dynamic scheduling strategy are proposed. A discrete-event model is constructed using the FlexSim simulation software. Through parameter calibration based on actual production data from 2022–2023, the effectiveness of the optimization scheme in improving equipment utilization and reducing buffer waiting time is verified, providing technical reference for the design of intelligent packaging lines for similar high-value and fragile materials. The proposed method and simulation framework are applicable to the optimization of production lines for imaging equipment and related materials.