The Yellow River Delta is a typical representative of a newborn estuarine wetland, and is also an important ecological function area in both the Bohai Sea and the Yellow River Basin. Studying the shellfish community structure in the intertidal zone of the Yellow River Delta is of guiding significance for assessing the ecological status of the Yellow River Delta. In this study, the benthic shellfish resources of eight sampling sections in the intertidal area of the Yellow River Delta were systematically investigated to identify the seasonal variation in shellfish diversity and community structure characteristics in the Yellow River Delta. The investigations were conducted during astronomical tide in four seasons, namely, summer in August 2022, autumn in October 2022, winter in February 2023, and spring in May 2023. Twenty-two shellfish species were identified and the species quantities and densities, the dominant species, and the dominant degree varied greatly among both seasons and sampling sections. Most species (16) and the highest density of 1203.96 ind/m² were observed in summer. The dominant species were Umbonium thomasi, Potamocorbula laevis, Moevella iridescens, and Mactra quadrangularis, with P. laevis being dominant in all seasons. The Shannon-Wiener diversity, Margalef richness index, and Pielou evenness index values were highest in spring. U. thomasi, P. laevis, Mactra quadrangularis, and Meretrix petechialis were the four species with the largest contributions to inter-community dissimilarity among sampling sections in all four seasons. The results show that the benthic shellfish resource in the intertidal area of the Yellow River Delta was largest in summer, but the community diversity was highest in spring. Our results provide basic data and a theoretical foundation for the protection, development, and utilization of wild shellfish resources in the Yellow River Delta.