To investigate the effects of bacteria-algae co-regulation on the plankton community structure in the aquaculture water of Chinese mitten crab (Eriocheir sinensis) in photovoltaic-integrated ponds, this study established three treatment groups: a photovoltaic group (FPI), a photovoltaic with bacteria-algae co-regulation group (FP-BA), and a traditional pond group (TAC). Through a 90-day dynamic monitoring period with sampling on days 0, 30, 60, and 90, and by combining morphological identification, dominance calculation, and Shannon-Wiener diversity index analysis, we systematically compared the community composite on and ecological characteristics of phytoplankton and zooplankton under different treatments. The results indicated that bacteria-algae co-regulation (FP-BA group) significantly optimized the phytoplankton community structure. Specifically, it effectively reduced the dominance of cyanobacteria such as Microcystis during the later culture stages, consistently maintained the highest phytoplankton diversity index, and promoted the development of beneficial algae such as green algae and diatoms. Concurrently, through a bottom-up effect, bacteria-algae co-regulation significantly enhanced the zooplankton community. The FP-BA group maintained the highest zooplankton density and diversity index during the mid-to-late culture stages, with a marked increase in the dominance of high-quality prey organisms such as large cladocerans (e.g., Daphnia) and copepods (e.g., Sinocalanus). In conclusion, bacteria-algae co-regulation can effectively steer the plankton community in photovoltaic-integrated crab ponds toward a more stable structure and optimized function, providing technical support for constructing a healthy and efficient "aquaculture-photovoltaic complementarity" ecosystem for Chinese mitten crab farming.