Abstract The wide-range applications of isotope analysis make isotope measurement approaches under attentive focus. Off-axis integrated cavity output spectroscopy technology (OA-ICOS) is the most advanced isotope analysis method; however, further studies are still needed to avoid signal noise and improve accuracy. Zero-phase low pass filtering multivariate Fourier Decomposition Method (FDM) was applied for data analysis in the present study, which has its unique advantage to fix up rapid but seasonal changes for nonlinear and non-stationary time series data. In the present study, δ13C content in gaseous CO2 sample were measured by OA-ICOS at ambient temperature. The experimental data treated by FDM showed less signal fluctuant and clearer value change tendency than what showed in raw data, whereas the data density kept same with that of raw data. In the meantime, the experimental results suggested that it is flexible to decide the variance explanation rate by simply change the order of an FDM filter. This approach meets up with the requirements of different practical application scenarios of isotope analysis, which enhances the feasibility for OA-ICOS application in real-time environmental monitoring field.