The open-path FTIR (OP-FTIR) is often used to measure the atmospheric gas composition and concentrations. The OP-FTIR, however, is sensitive to the changed ambient factors, which likely led to quantitative biases. This study developed methods to minimize the effect of the ambient temperature and humidity on N2O/CO2 quantification. These methods can help the users who implement the OP-FTIR to estimate gas fluxes in the agroecosystem achieve more precise and accurate estimations.