It's necessary to remove the baseline from the spectra, which measured by open-path Fourier transform infrared spectrometry, for further spectral analysis such as qualitative and quantitative analysis. An automatic baseline correction method, the Iterative Averaging method, is presented. Baseline corrected by this method is accurate, and it also shows more precise than other methods when it is applied to Fourier Transform Infrared experimental spectra and simulated data. This method solves the key technology of the real-time on-line spectral analysis of OP-FTIR and improves the capability and adaptability of the unsupervised on-line system effectively. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement