Previous research rarely considers the biogeochemistry process of the whole rock weathering layer-soil profile. The aim of Critical Zone science is re-understanding the structure and function of ecosystems from the canopy to bedrock, which emphasizes the relationship of material and energy between atmosphere and plant, between plant and soil, between soil and river in small watershed on the watershed scale. Carbon fixation and allocation are the key starting processes. Decomposition and transformation of soil carbon are the key turnover processes. Carbon migration and balance in small watershed are the key transfer processes. Further research is needed in the process, mechanism and ecology function of ecosystem carbon cycle from the canopy to bedrock based on the watershed scale. Carbon isotope technology has the function of indication, tracing and integration. Based on the ¹³C natural tracing and artificial labelling methods, we can further understand the process and mechnism of carbon biogeochemistry.