The black soil in northeast China is facing the threat of continuous deterioration. The carbon cycle plays a critical role in the maintenance of soil fertility and productivity in farmland, where microorganisms regulate the carbon balance in soil. This review summarizes the distribution, characteristics, and degradation of black soil. Firstly, it describes the transformation pathways and community composition of carbon-fixing microorganisms in the black soil in farmland. These microorganisms employ six pathways to fix carbon. The high-throughput sequencing with the carbon fixation gene cbbL as the probe reveals that the carbon-fixing microorganisms in the black soil of northeast China mainly belong to Proteobacteria and Cyanobacteria. Secondly, the review discusses the effects of tillage systems, fertilization, straw return, and freezing-thawing on microbial carbon fixation in black soil. Finally, the contributions of carbon-fixing microorganisms to agriculture and the environment are expounded from increasing crop yields, reducing agricultural non-point source pollution, and reducing greenhouse gas emissions. While these microorganisms are crucial for nutrient recovery and crop yield improvement, research remains to be carried out. The protection and utilization of black soil necessitates a deeper understanding of the microbial resources involved in carbon fixation. Interdisciplinary studies should be carried out to reveal the ecological processes and function and structure changes of these microorganisms, and a black soil management scheme focusing on microbial carbon cycling should be formulated for the protection and utilization of black soil.