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The Yellow River estuary is one of the three largest estuaries along the coastal waters of China, along with the Yangtze and Pearl River estuaries. Its adjacent seawaters are rich in biological resources, with abundant fish habitat, spawning grounds, and migration channels in the Bohai Sea and the Yellow Sea. However, as the waters are too shallow for a survey ship, data was insufficient for research in the intertidal zone of the salt and freshwater interchange. Instead, by interviewing and analyzing the daily catches by the set net of the local fishermen, this study explored the fishery biodiversity in the intertidal zone of the Yellow River estuary from April to November 2020. Yellow River estuary is rich in fishery resources, especially small fishery organisms and fish recruitment stocks. There were monthly variations in the dominant species composition and biodiversity index. A total of 61 species were recorded, most of which were fish and crustaceans. The diversity, evenness, and species richness index increased in summer (July and August) and decreased in autumn (October and November). By cluster analysis of the species compositions, the surveyed months can be divided into two groups: May to September, and October to November. Lateolabrax maculatus and Liza haematocheila were the most common and dominant species in all surveyed months. The main contributors to the catch of each month were: snails from April to July, snails and fish in August, fish in September, and crabs from October to November. Catches by the set net were mainly composed of individuals with body mass < 2 g from April to September. From body mass-frequency distributions, fish with body mass < 10 g were the main contributors to total catches from April to September. The mean body mass of fish in all surveyed months was 13 g/ind.. The dominant fish species with body mass with < 20 g were: Gobioidei in April; L. maculatus in May; Konosirus punctatus in June; Pennahia argentata, Gobioidei, and L. haematocheila in June to August; and Sardinella zunasi, Thrissa kammalensis, T. mystax, Sillago sihama, Tylosurus melanotus, Gobioidei, and L. haematocheila in September. From the above results, the local set net fishery survey proved to be an effective method of collecting fishery data in the intertidal zone and can be incorporated in studies considering the distribution of fishery resources and breeding grounds in the seawaters adjacent to estuaries. In addition, this study provided clear evidence that set net fishing practices could severely impact the natural recruitment and stock enhancement of fish resources due to the low selectivity of nets and the overlap with larval fish migration channels. The number of larval fish captured by the set net fishery was, roughly estimated, several times higher than the local enhancement released. To minimize the effects of net mesh size, considering the spatial-temporal distributions of fish larvae, set net fishing practices should be concentrated to summer and early autumn, though further research is required to comprehensively account for both the protection of fishery resources and livelihoods.