The Andaman Coastal Sea provides a rich resource of seafood as well as a major contribution to the socio-economy of many local communities in Thailand. The aim of this study is to model food web structure and estimate energy flow through trophic levels using the Ecopath tool. Data have been collected on fish length, weight and diet composition from three provinces, Krabi, Phuket and Phangnga along the Andaman Sea coast of Thailand. Data from commercial as well as artisanal fishing ports were entered into the model. The model computed data for trophic level, food web structure, and ecological function of functional groups. The results indicate that the coastal ecosystem of the Andaman Sea is composed of five aggregated trophic levels of 46 functional groups, ranking from 1.0 to 4.227. The total system throughput is 9162.513 t km−2 y−1 and internal consumption, respiration, flow into detritus, and export out of the system accounts for 28.83%, 16.06%, 28.34%, and 26.77%, respectively. The Mixed Tropic Impact (MTI) shows detritus and low trophic level groups make a significant contribution to the diet of groups at higher trophic levels. Planktivorous fishes are important components of food web structure. The total system throughput analysis indicates that the ecosystem is in a relatively immature state. Pedigree analysis showed that the model has high reliability. The application of the model for fisheries management is discussed. In particular, the use of the model for local Fisheries Improvement Projects is recommended.