Aiming at the interference caused by the gas in the air gap between the gas cell and the spectrometer, as well as the baseline drift and distortion in the application of Fourier infrared spectroscopy on-line analysis of dissolved gas in transformer oil, a new method of gas absorption spectrum compensation based on time-sharing scanning with two gas cell, was proposed. Based on the traditional single-gas cell measurement, a background gas cell is added that is the same as the structure, size, and other parameters of the measurement gas cell. The background gas cell is filled with nitrogen, and the measurement gas cell is filled with the sample gas to be measured. Besides, the controller is used to realize the switching control of the background gas cell and the measurement gas cell. However, the spectrum processed by the conventional absorbance calculation formula has unknown absorption peaks in the wavenumber range of 1 100 to 1 200 cm^-1. There is a severe baseline drift phenomenon, which indicates that the calculation method is no longer suitable for double gas cells. Therefore, in order to eliminate the adverse effect of the inconsistency of the parameters between the two gas cells, especially the difference in the filter characteristics of the window, a new method for calculating the gas absorption absorbance spectrum based on the double gas cell time-division scanning is further proposed, which was proved to eliminate unknown absorption peak and baseline drift, and the drift value decrease from 0.3 to 0.005. Finally, a transformer oil sample was obtained at a substation in Shaanxi, and the corresponding gas samples were obtained after degassing treatment. Conventional single-cell scanning method (group 1), two-gas cell compensation method (group 2), and gas chromatography (group 3) were used for experiments. The results show that methane concentration in group 1 is always more significant than that in group 2. At the same time, the carbon dioxide concentration in group 1 is always greater than the carbon dioxide concentration in group 2. The obvious difference in such analysis results is most likely due to the influence of the air gap between the spectrometer and the gas cell. On the whole, compared with group 1, the analysis results of group 2 are closer to those of gas chromatography. In summary, the new gas absorption spectrum compensation method based on double gas cell switching time-sharing scanning proposed in this paper can effectively solve the problem of spectral baseline drift and distortion. In gas analysis, this method can eliminate the influence of interfereing gas between the gas cell and the spectrometer, and obtain more accurate analysis results.