This study aimed to explore the distribution patterns of the phylogenetic structure of fish communities and the maintenance mechanism of fish diversity at different spatio-temporal in the Yellow River estuary and its adjacent waters and discuss the main influencing factors affecting community assembly. This study focused on the fish communities in the whole area of the Yellow River estuary and its adjacent waters and used the net relatedness index (NRI) to analyze the spatio-temporal changes in the phylogenetic structure of the fish community, considering the phylogeny of fish species based on data collected from different surveys. The surveys were conducted in June, July, August, and October 2013; and February, April, and May 2014 in the Yellow River estuary and its adjacent waters from 2013 to 2014 The results showed that in the whole area of the Yellow River estuary and its adjacent waters, community structures in February and April 2014 were phylogenetically overdispersed, and competitive exclusion may be the main influencing factor in community assembly. Meanwhile, in other months, the community structures were phylogenetically clustered, and habitat filtering may be the dominant factor in the community assembly of fish assemblages. The fish communities were phylogenetically clustered, and habitat filtering might have played a major role in the phylogenetic structure of fish communities at each station throughout the year, except for the phylogenetic structure of fish communities at stations near the estuary, which showed that phylogenetic overdispersion and competitive exclusion played a dominant role. The NRI of fish communities among different stations varied slightly each month, and the community structures at most stations were phylogenetically clustered in different months, except for February and April 2014, indicating that habitat filtering was the main driving factor. Fish communities have different species compositions and phylogenetic structures at different spatiotemporal scales in the Yellow River estuary and its adjacent waters. Habitat filtering played a dominant role in phylogenetic structure at large spatio-temporal scales, whereas competition exclusion was the main driving factor in the phylogenetic structure at small spatio-temporal scales.