Flow electrode capacitive deionization (FCDI) is a simple and efficient desalination technology but is limited by high energy consumption due to the high resistance of the flow-electrode. In this study, we simulated the collision and charge transfer processes within the flow-electrode using a CFD-DEM-based two-phase flow model. The model accurately simulated the conductivity of flow-electrodes in both long straight and serpentine channels under various flow rates and carbon loadings, revealing that particle-collector collisions play a decisive role in electrode conductivity. Based on these findings, we proposed two optimized flow channels to increase the effective collisions between carbon particles and collector plates: a serpentine channel with a central cylindrical obstacle (FCDI-O) and a zigzag-shaped channel (FCDI-Z). The results demonstrate that both FCDI-O and FCDI-Z significantly enhance flow-electrode conductivity (80.4% for FCDI-O and 188.3% for FCDI-Z) and reduce desalination energy consumption (21.3% for FCDI-O and 25.1% for FCDI-Z), compared to the original FCDI serpentine channel. We further analyzed the energy consumption distribution across FCDI components using a steady-state electrochemical model. The results indicate that, under various operating conditions, the total energy consumption decreases, and the proportion of energy consumed by the flow-electrode is lower in the FCDI-Z channel than in the FCDI-O channel. However, the flow-electrode remains the largest energy consumer in the FCDI desalination process. This study provides valuable insights for the development and practical application of new flow channels for FCDI desalination.