Swimming crab (Portunus trituberculatus) are an important aquaculture species in eastern coastal areas of China. To improve the understanding of P. trituberculatus culture ecosystem functioning, the dynamics of energy flow and trophic structure of a P. trituberculatus polyculture system (co-culture with white shrimp Litopenaeus vannamei and short-necked clam Ruditapes philippinarum) were investigated in this study. Three Ecopath models representing the early, middle, and late culture periods of a P. trituberculatus polyculture ecosystem, respectively, were constructed to compare ecosystem traits at different culture periods. The results demonstrated that detritus was the main energy source in this polyculture ecosystem, and most of the total system throughput occurred at trophic levels I and II. Artificial food input and consumption by the culture organisms increased from early to middle and late periods, which produced marked impacts on biomass structure and primary production. R. philippinarum was considered to have a dominant influence on phytoplankton community dynamics which changed from nano- to pico-phytoplankton predominance, from the middle to the late period. Considering the low utilization efficiency of pico-phytoplankton production, large amounts of detritus accumulated in the sediment in the late period, which may constitute a potential risk for the ecosystem. Ecological network analyses indicated that the total energy flow and level of system organization increased from the early to the middle and late periods, whereas food web complexity and system resilience decreased from early to middle and late periods, which may indicate a trend of decreasing ecosystem stability. The system may be further optimized by increased stocking density of R. philippinarum and by introducing macro-algae at a suitable biomass to increase ecosystem stability, energy utilization efficiency, and aquaculture production.