Soil carbon sequestration has been one of most important research frontiers of soil science for the last decade. However, carbon sequestration for sustainable management is being urged by both climate change mitigation and global soil degradation. In this review paper, the ecosystem functioning and ecological services of soil organic carbon were emphasized. Sequestration of organic carbon was in depth examined by linking to bioactivity and ecosystem functioning of soil. Current knowledge on variation of soil bioactivity with soil carbon sequestration was overviewed and synthesized, particularly at micro-scale of soil aggregates. Taking rice paddy soil as an example, co-evolution of microbial community and diversity, and soil functional activity with soil organic matter build-up at soil aggregates level was analyzed in terms of soil development. Furthermore, were highlighted the emerging issue on characterizing the coupling of bioactivity with carbon sequestration, the nature of sustainable soil carbon sequestration by means of micro-aggregate scale interaction of organic matter-microbe-enzyme activity, and the best management practices for attaining the sustainable carbon sequestration. All these issues could be pursued with the help of non-destructive soil aggregate fractionation and in situ microscale supermicroscopic observation technologies. Therefore, soil research on carbon sequestration versus bioactivity at microscale will enhance systematic understanding of ecosystem functioning and services provided by soil organic carbon, in order to provide sound knowledge base for rational organic matter management and sustainable carbon sequestration, and for policy making aiming at enhancing crop productivity and environmental services as well as climate change mitigation.