Artificial reefs are crucial for coastal ecological restoration, yet their long-term ecological effects and evolutionary mechanisms remain largely unknown. This study analyzed the structural and functional changes of artificial reef ecosystems in the national marine ranching demonstration area of Haizhou Bay (Jiangsu Province, China) by constructing ecosystem models for 2003 and 2023 using the Ecopath with Ecosim (EwE) framework. The Ecopath results indicated that total system throughput (TST) increased by 26% from 2003 to 2023, rising from 1212.63 to 1526.32 t/km²/year. Trophic transfer efficiency (TTE) improved from 13.7% to 15.16%, and system maturity also increased, with the primary productivity to respiration ratio (PP/R) changing from 7.08 to 7.43 and the system organization index (SOI) moving from 0.238 to 0.284. Notably, the keystone species shifted from Sciaenidae in 2003 to Oratosquilla oratoria in 2023. However, trawling operations continued to suppress high-trophic-level species, such as conger. Ecosim scenario simulations suggested that banning trawling could enhance the recovery of higher-level consumers like congers. Despite this, most species showed a declining biomass trend due to increased intraspecific competition. The findings demonstrate that while artificial reefs can enhance ecosystem function by boosting primary productivity and energy transfer efficiency, trawling still poses a significant barrier to the recovery of ecosystem status. To address these challenges, it is recommended to implement stricter controls on fishing gear, optimize policies by establishing no-fishing zones, improve reef structures to enhance energy transfer efficiency, and maximize the utilization of basic resources. Regular stock enhancement activities should be conducted to adjust the proportions of dominant species, such as O. oratoria. Additionally, ongoing ecological monitoring and assessments of management effectiveness are essential to balance ecological restoration with the sustainable use of fishery resources, providing a scientific framework for effective marine ranching management.