This paper proposes two types of seawater-coolant feed arrangements of a heat recovery unit (HRU) for improving the performance of a multi-stage vacuum membrane distillation (VMD) system: backward feed (BF) and parallel feed (PF). Theoretical studies were performed to assess the effect of the BF and PF feed arrangements on the system performance. In addition, to comprehensively understand the thermochemical phenomena in both the BF and PF arrangements, spatial variations in the temperature, permeate pressure, permeate flux, and salinity were investigated using a rigorous simulation model that considered the heat and mass transfer across the hollow fibers coupled with the transport behavior on the feed side. To determine the superior HRU configuration between BF and PF, the water production, recovery ratio, and specific energy consumption of the multi-stage VMD system were investigated. It was found that the total water production in the PF arrangement was approximately 2.94 m3/d, which was approximately 6% higher than in the BF arrangement; however, the BF arrangement was more efficient for the production of freshwater than the PF arrangement when a smaller number of module stages was employed. Furthermore, the optimum number of HRUs in the BF arrangement was determined based on this theoretical study.