Microorganisms play a key role in aquatic ecosystems. Recent studies have showed that some keystone taxa in microbial communities can drive the changes in community composition and function. However, most studies have focused on abundant taxa, whereas rare taxa are neglected because of their low abundance. Therefore, it is important to clarify the seasonal variation of bacterial and microalgal communities and understand the synergistic adaptation of these organisms to different environmental factors. We investigated the bacterial and eukaryotic phytoplankton communities and their seasonal co-occurrence patterns using16S and 18S rDNA sequencing approach. Our results indicated that in eukaryotic phytoplankton networks, spring and autumn networks had higher connectivity and complexity, forming the highly stable community structure. The positive interactions of bacterial network were significantly higher than the negative interactions, indicating that more mutual cooperation can make the microbial communities better resist changes in the external environment, thereby maintaining the stability of microbial network. The main genera identified as keystone taxa in bacterial networks were Pseudomonas, Stenotrophobacter, Bosea, and Hyphomicrobium, which were significantly related to many predicted functions. The main genera identified as keystone taxa in eukaryotic phytoplankton networks were Monodus, Tetradesmus, Scenedesmus, Monoraphidium, and Amphora, which were affected by dissolved organic carbon, nitrate, nitrite, and phosphate, changes in these environmental factors can affect the stability of network. Through the co-occurrence patterns, we analyzed the internal mechanism of interaction between bacteria and eukaryotic phytoplankton and understood the potential importance of keystone taxa in ecological processes such as carbon, nitrogen, and phosphorus dynamics.