Paddy rice soil, derived from long-term rice planting, is a type of artificial soil. Studies of paddy rice soil in China reflect the international status of Chinese soil science based on the long history and importance of rice cultivation. Paddy soil is a classical model for studying soil biogeochemical processes. Investigation of biogeochemical cycles, and the coupling and driving mechanisms of key elements (carbon, nitrogen, phosphorus, sulfur, iron, etc.) in paddy soil is important in soil biology studies. Therefore, in this study, on account of the International Year of Soils, we review some achievements of the "Soil biology development strategy research" project funded by Academician Bureau of Chinese Academy of Sciences, and discuss the biogeochemical cycles of key elements (carbon, nitrogen, phosphorus, sulfur, iron, etc.) in paddy ecosystems and the microbial regulation mechanisms of their coupling. We emphasize the basic biochemical features of paddy soil, the coupling processes of C-N, C-N-P, C-N-Fe, and other processes in paddy soil, as well as its microbial feedback regulation mechanism. We also propose perspectives for the development of future studies on the microbial driving mechanisms of the biogeochemical cycles of key elements in paddy soil.