The paddy field ecosystem carbon cycle is a significant part of the terrestrial ecosystem carbon cycle in China. The organic carbon cycle in paddy soil (including processes such as input, allocation, and stabilization) is driven by biochemical processes that are dominated by microbes, and is the core of soil carbon cycle research. Current studies on paddy soil carbon cycle processes and their mechanisms lack metrology-level research based on the basic theories of chemistry, biology, and ecology. Therefore, systematic and quantitative analysis of the key processes in the paddy soil carbon cycle, which includes chemical-biological-environmental elements, deal with the bottleneck for the comprehensive evaluation of the carbon-sink-adding/emission-reduction effects of paddy fields, as well as the in-depth study of the current problems of soil biochemistry (such as the soil carbon cycle and soil fertility and greenhouse gas emissions). Based on a comprehensive analysis of the basic connotation of metrology and the development demands of soil metrology. This paper describes how paddy soil has an obvious discriminative soil genesis and biochemical characteristics that differ from other soil types. The paper mainly focuses on three processes of the paddy soil carbon cycle: (①measurements of key microbial processes involved in fresh organic matter transformation and mineralization in paddy soil, ②measurements of key microbial processes involved in CH4 generation in typical paddy soil, and ③measurements of microbial CO2 photosynthesis and assimilation functions in typical paddy soil. Based on these measurements, we discuss the application of statistical and mathematical models of soil biochemical processes to soil metrology research and put forward the metrological development trend and the prospects of scientific issues in the research on the metrological characteristics of key microbial biological processes in the paddy soil carbon cycle. It is hoped that these discussions will promote the construction of basic theories in the research field and contribute to the development of new technologies in China.