Hydrological fluctuations (HFs) are a core characteristic of wetland ecosystems and are intensifying under global climate change, profoundly affecting soil microbial community structure and the associated carbon (C) cycling processes. However, the mechanisms underlying microbial community responses to HFs and their regulatory effects on wetland soil C sequestration and emission remain unclear. This study conducted a 4-year in-situ manipulation experiment in the Baiyangdian Wetland (a typical freshwater wetland in North China) to explore the effects of different hydrological fluctuation patterns (static flooding, moderate fluctuation, and extreme fluctuation) on soil bacterial and fungal communities, as well as their C cycling functions. High-throughput sequencing, microbial functional prediction, and soil C fraction determination showed that HFs significantly altered microbial community composition, diversity, and co-occurrence network structure. Compared with static flooding, moderate and extreme HFs reduced bacterial alpha diversity (Shannon index decreased by 12.3% and 21.5%, respectively) but increased fungal alpha diversity (Shannon index increased by 8.7% and 15.2%, respectively). The microbial co-occurrence network under extreme HFs showed lower complexity (node number decreased by 38.6%) and stability (modularity decreased by 25.3%) than static flooding. Taxonomically, HFs promoted the enrichment of anaerobic taxa (e.g., Deltaproteobacteria, Methanomicrobia) and inhibited aerobic taxa (e.g., Actinobacteria, Alphaproteobacteria). Functionally, moderate HFs enhanced the abundance of functional genes related to recalcitrant C decomposition (e.g., laccase, cellulase), while extreme HFs significantly increased methanogenesis-related genes (e.g., mcrA) and reduced C fixation genes (e.g., cbbL). Redundancy analysis revealed that soil redox potential (Eh), water-filled pore space (WFPS), and dissolved organic carbon (DOC) content were the key drivers of microbial community changes. Structural equation modeling indicated that HFs regulated wetland soil C sequestration capacity mainly by altering microbial community composition and functional gene abundance. This study clarifies the response patterns and functional consequences of soil microbial communities to HFs in wetlands, providing a theoretical basis for predicting wetland C cycle dynamics under future climate change scenarios.