Lake is one of the major ecosystems on the earth. Lake ecosystems play an important role in the nutrient cycling in the regional as well as in the global scale due its connection with different interfaces and its functioning as a junction in the catchment. Microbes are key biological components of the lake ecosystems and are the major forces driving the cycling of nutrients including the carbon. Lake ecosystems particularly in shallow lakes always possess two alternative stable states, a turbid state dominated by phytoplankton and a clear state dominated by submersed macrophyte. Such a change of alternative states is always related to the loading of nutrients including phosphorus and nitrogen as a result of human activities and global change. The shift of alternative states has strong impacts on the ecosystem structure and its function. In this review, we focused on responses of microbial community structure under the regime shift between clear state and turbid state, and subsequently the change of microbial carbon cycling driven by the microbes in lakes. Based on these analyses, we further point out the major research priorities in this direction in the future. We hope such a review will be helpful for a better understanding on the carbon cycling and its mechanisms driven by microbes in lakes.