Based on phytoplankton net samples from the Bohai Sea from 1959 to 2015, the long-term changes in species composition, cell abundance, community structure, and species diversity were analyzed. A total of 77 genera and 170 taxa were recorded, most of which were temperate-coastal ecotype species. The composition pattern of the dominant taxa changed dramatically over the fifty-plus years. Centric diatoms such as Chaetoceros spp. and Coscinodiscus spp. dominated in the communities of last century, while Paralia sulcata, Thalassionema spp., and dinoflagellates such as Noctiluca scintillans and Tripos spp. gradually became predominant in this century. The cruise-averaged cell abundances ranged from 8.33 × 104 cells/m3 to 472 × 104 cells/m3, with diatoms accounting for 65.3%~99.8%. The abundances and species diversities declined to their lowest levels last century, whilst they had 1.5 times and 15.0% respective recoveries in this century. The persistent increase in seawater N∶P ratios in the Bohai Sea has led to a phytoplankton transition from diatom-dominated communities to communities co-dominated by diatoms and dinoflagellates, with an increase of 2.82 times in the ratio of diatoms to dinoflagellates in this century from that in the last century. The decadal changes in the phytoplankton community structure and its herbal diet basis in the Bohai Sea affect the recruitment process during the early life stages of the key resource species. This study provides a baseline database and references for discussion on the mechanisms of adaptive responses of fishery populations to the long-term environmental changes in the Bohai Sea.