<p>To investigate changes in phylogenetic diversity of fish communities and the Maintenance mechanisms over the past 30 years in the Yellow River estuary and its adjacent waters, long-term changes in phylogenetic α and β diversity and the phylogenetic structure of fish communities under both the local and regional species Pools were examined based on data collected from multiple sources from 1990 to 2023. The Phylogenetic α diversity exhibited a significant decline over the past 30 years, with a more pronounced decrease under the local species pool compared to the regional species pool. While phylogenetic β diversity showed minor differences between the two species Pools, it demonstrated consistently high across different years and over the 30-year period, regardless of whether multi-site dissimilarity or pairwise dissimilarity calculation methods were used. The turnover component drove changes in phylogenetic β diversity within the fish community, revealing significant differences in the composition of fish phylogenetic structure across different years in the waters. As for the phylogenetic structure index, the mean pairwise distance (<i>MPD</i>) exhibited a declining trend, while the mean nearest taxon phylogenetic distance (<i>MNTD</i>) showed an increasing trend over the study period. Both indices were higher under the local species pool compared to the regional species pool, and the standardized effect sizes of both indices showed significant increasing trends under both species pools. It suggests that the fish communities gradually became phylogenetically clustered, with a higher degree of clustering observed under the local species pool compared to the regional species pool. The phylogenetic α and β diversity, as well as the phylogenetic structure of fish communities, have changed over the past 30 years, with environmental filtering emerging as the primary factor influencing fish community assembly in the waters.</p>