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The Microwave Radiation Imager (MWRI) onboard the FengYun satellite plays a crucial role in global change monitoring and numerical weather prediction. Estimating and correcting geolocation errors are important to retrieving accurate geophysical variables. However, the instantaneous field of view (IFOV) inter-channel deviation, which is mainly caused by the structure mounting error and measurement error of feedhorns, is less studied. In this present study, we constructed a general theoretical model to automatically estimate the IFOV inter-channel deviations suitable for conical-scanning instruments. The model can automatically detect the along-track and across-track vectors that pass through the land–sea boundary points and are perpendicular to the actual coastlines. Regarding the midpoints of the vectors as the brightness temperature (Tb) inflection points, the IFOV inter-channel deviation is the pixel offset or distance of the maximum gradients of the Tb near the inflection points for each channel relative to the 89-GHz V-pol channel. We tested the model’s operational performance using the FY-3G/MWRI-Rainfall Mission (MWRI-RM) observations. Considering that parameter uploading adjusted the IFOV inter-channel deviations, the model’s validity was verified by comparing the adjustments calculated by the model with the theoretical changes caused by parameter uploading. The result shows that the differences between them for all window channels are less than 100 m, indicating the model’s effectiveness in evaluating the IFOV inter-channel deviation for the MWRI-RM. Furthermore, the estimated on-orbit IFOV inter-channel deviations for the MWRI-RM show that all channel deviations are less than 1 km, meeting the instrument’s design requirement of 2 km. We believe this study will provide a foundation for IFOV inter-channel registration of passive microwave payloads and spatial matching of multiple payloads.