Technical Abstract: From the point of view of biogeochemistry, manure is a complex of organic matter containing minor minerals. When manure is excreted by animals, it undergoes a series of reactions such as decomposition, hydrolysis, ammonia volatilization, nitrification, denitrification, and fermentation from which carbon dioxide, nitrous oxide, methane, and ammonia can be produced. Based on the principles of thermodynamics and reaction kinetics, these reactions are commonly controlled by a group of environmental factors such as temperature, moisture, redox potential, pH, and substrate concentration gradient. The relations among the reactions, the environmental factors and gas production have been incorporated in a process-based model, Manure-DNDC, to describe manure organic matter turnover and gas emissions. Manure-DNDC was constructed by integrating five farm components (i.e., feedlot, liquid and solid manure treatment/storage, anaerobic digester and cropping field). Manure-DNDC calculates variations of the environmental factors for each component based on its technical specifications, management practices, and the weather and soil conditions; and then utilizes the environmental parameters to drive the biogeochemical reactions. To verify the applicability of Manure-DNDC for livestock farms, seven datasets of air emissions measured from farms across the U.S. plus a pasture in Scotland were used for model evaluation with encouraging results. A dairy farm in New York was used to assess the impacts of alternative management practices on mitigation at a farm scale. The modeled results showed that changes in management practices could reduce greenhouse gas emission by 30% and ammonia emission by 36% at the farm scale.