Abstract: Coastal ecosystems in the Bohai Sea and the Yellow River Estuary support vital fishery resources but are increasingly threatened by environmental degradation and anthropogenic pressures, necessitating reliable and cost-effective monitoring. To establish an accurate and efficient fishery resource monitoring system and address the contradiction of "insufficient accuracy" and "high cost" in traditional surveys of the coastal waters of the Bohai Sea and the Yellow River Estuary, this study utilized the fishery resource survey data from May and August in 2023 to 2025, compared the efficacy of three sampling methods: simple random sampling, cyclic systematic sampling, and stratified random sampling, and through quantitative analysis using the multi-objective comprehensive evaluation index (C_REE), determined the optimal sampling scheme that balances accuracy and economy. The study found ① the ranking of sampling method efficacy is consistent, with stratified random sampling having the lowest C_REE and the strongest stability; ② the stratification criteria are determined by region and season: in May of the Bohai Sea coastal area, it is ≤10 m、10-20 m、>20 m; in August, it is ≤8 m, 8-18 m, >18 m; in May of the Yellow River Estuary, it is ≤8 m, 8-18 m, >18 m; in August, it is ≤6 m, 6-16 m, >16 m; ③ under the high accuracy standard of C_REE ≤10%, approximately 35 stations are needed for the Bohai Sea coastal area in May and August of a single year; for the Yellow River Estuary in May and August of a single year, approximately 18 stations are needed; if the conventional standard of C_REE ≤15% is adopted, the number of stations can be reduced by approximately 37.5%. The research results can provide technical support for the construction of a long-term monitoring system for fishery resources in the Bohai Sea coastal area and the Yellow River Estuary, and also provide scientific basis for the optimization of sampling schemes for the river-mouth-nearshore composite ecosystem in the north.