This study proposes a self-calibration method based on zoned reference transfer for real-time temperature monitoring of the Fengyun-4 (FY-4) Microwave Satellite payload. It aims to correct the effects of calibration coefficient degradation and instrumental background drift in uncooled infrared temperature measurement systems during on-orbit operation. The method dynamically updates the calibration reference through alternate observations of a Fixed External Blackbody and an Insertable Internal Blackbody within the field of view. Concurrently, it utilizes Masked Zone pixels to sense and compensate in real-time for the common-mode background drift caused by camera temperature variations. This approach jointly ensures long-term measurement stability and instantaneous accuracy without the need for complex scanning mechanisms. Ground validation experiments demonstrate that the proposed method suppresses background radiation drift by over 72%. Under dual-camera cross-validation, the equivalent blackbody temperature retrieval errors for low-temperature targets (230–250 K) were significantly reduced from approximately 3 K to roughly 0.4 K. Furthermore, based on a comprehensive uncertainty budget, the absolute expanded uncertainty is evaluated to be better than 0.87 K (k = 2) at 300 K. The proposed method provides a reliable and compact technical solution for high-precision infrared thermometry of moving components on-orbit.