Crop assimilative carbon, which is an important part of the carbon cycle of the "atmosphere-plant-soil" system and also an important source of soil organic carbon, is closely linked to the rhizosphere environment and crop growth. However, because crop assimilative carbon is both complex and variable, the fate of this part of the carbon cycle is still poorly understood. The biogeochemical processes involved in the distribution, transformation, and stability of assimilative carbon significantly affect the carbon cycle in terrestrial ecosystems globally. In this study, we accordingly summarize the distribution, transformation, and stabilization mechanisms of crop assimilative carbon and its contribution to soil organic carbon; discuss the distribution and adjustment system of assimilative carbon in the rhizosphere-aboveground soil system; analyze the characteristics of microbe-assimilative carbon interactions; and explain the relationship between assimilative carbon and the establishment of soil microbial diversity. We propose focusing on the quantitative study of crop assimilative carbon, including its distribution within the soil-crop system in different ecosystems and on improving the understanding of carbon cycling processes in terrestrial ecosystems. We also highlight the importance of the mechanism of assimilative carbon transfer and distribution to the soil carbon pool. Finally, we describe how nanometer secondary ion mass spectrometry technology, combined with microscope imaging and isotope tracer technology, and a combination of molecular microbiology and community ecology techniques, can be effective means for studying the biogeochemical characteristics of crop assimilative carbon.