Microorganisms in sediments are an important part of the aquatic ecosystem, and their functional activities are sensitive to external environmental pressure. Shallow lakes are characterized by frequent sediment resuspension events, leading to large amounts of nutrients being released. However, information about the potential impacts of sediment resuspension events on the functional activities of microbial communities is limited. In this study, the responses of microbial carbon metabolism in sediments under different wind–wave disturbance were analyzed by BIOLOG ECO microplates. The results showed that under four disturbance conditions (wind speeds of 0, 1.60, 3.62, and 14.10 m/s), the total carbon metabolism function of the sediment microbial community (represented as average well-color development, AWCD) remained unchanged (p > 0.05), and the final total AWCD value stabilized at about 1.70. However, compared with the control group, some specific carbon sources (e.g., amines and carboxylic acids) showed significant changes (p < 0.05). We found that short-term (8 h) resuspension events did not affect the total carbon metabolism of sediment microbial communities, while it affected the microbial utilization ability of some specific types of carbon sources. For example, we found that the microbial utilization capacity of polymers in the 14.10 m/s group was the best. This study provides a new insight into the carbon cycle process of shallow lake sediments that resuspension events will affect the carbon cycle process of sediments.