In order to guarantee the long-term on-orbit polarimetric measurement accuracy of scanning polarimeter, the onboard calibration mechanism and method of scanning polarimeter are studied. First, the system detection matrix is derived according to the technical characteristics of aperture-division and amplitude-division and with the consideration of practical error sources. Second, the onboard polarimetric calibration equation is deduced according to the instrument parameters and by use of the linearly polarized light and the non-polarized light with the known polarization states. Third, the linear polarization and non-polarization calibrators are designed for the onboard polarimetric calibration. Finally, the radiometric calibration data with the known polarization degree from the onboard solar diffuser is proposed to correct the low polarimetric measurement accuracy and stability. The proposed onboard polarimetric calibration method possesses the characteristics of high precision, high frequency, high efficiency, and so on, which can satisfy the application requirement that the long-term on-orbit polarimetric measurement accuracy is 0.005.