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In this paper, we investigated the dynamics of the interaction between Microcystis aeruginosa and filter-feeding fish in a new aquatic ecological model and considered the effects of aggregation and harvesting and focused on studying the critical threshold conditions through the analysis of saddle-node bifurcation, Hopf bifurcation, and Bogdanov–Takens bifurcation. We also conducted numerical simulations to illustrate our findings and provided biological interpretations. The results obtained indicate that the aggregation effect or harvesting can disrupt the coexistence of Microcystis aeruginosa and filter-feeding fish. The filter-feeding fish population may go extinct while the Microcystis aeruginosa population could survive. We identified the importance of finding an appropriate timing for harvesting Microcystis aeruginosa in order to promote the growth of the filter-feeding fish population. This optimal timing may be influenced by the carrying capacity of Microcystis aeruginosa. Taken together, our study sheds light on the dynamics of Microcystis aeruginosa and filter-feeding fish in an aquatic ecosystem, highlighting the critical role of aggregation, harvesting, and timing in determining the coexistence and survival of these species.