Global climate change is one of the most important issues of contemporary environmental safety. A scientific consensus is forming that the emissions of greenhouse gases, including carbon dioxide, nitrous oxide and methane, from anthropogenic activities may play a key role in elevating the global temperatures. Quantifying soil greenhouse gas emissions is an essential task for understanding the atmospheric impacts of anthropogenic activities in terrestrial ecosystems. In most soils, production or consumption of the three major greenhouse gases is regulated by interactions among soil redox potential, carbon source and electron acceptors. Two classical formulas, the Nernst equation and the Michaelis–Menten equation, describe the microorganism-mediated redox reactions from aspects of thermodynamics and reaction kinetics, respectively. The two equations are functions of a series of environmental factors (e.g. temperature, moisture, pH, Eh) that are regulated by a few ecological drivers, such as climate, soil properties, vegetation and anthropogenic activity. Given the complexity of greenhouse gas production in soils, process-based models are required to interpret, integrate and predict the intricate relationships among the gas emissions, the environmental factors and the ecological drivers. This paper reviews the scientific basis underlying the modeling of greenhouse gas emissions from terrestrial soils. A case study is reported to demonstrate how a biogeochemical model can be used to predict the impacts of alternative management practices on greenhouse gas emissions from rice paddies.