The 2nd Chinese Ocean Color and Temperature Scanner (COCTS2) is a key payload onboard the new-generation ocean color observation satellite Haiyang-1E (HY-1E). COCTS2 has three thermal emissive bands (TEBs). To ensure the stability and accuracy of the TEB, COCTS2 is equipped with onboard high-temperature and low-temperature blackbodies combined with the view of deep space to calibrate TEBs on-orbit. The COCTS2 on-orbit calibration method with the use of the Infrared Atmosphere Sounding Interferometer (IASI) data to correct the angular variation of reflectance of half angle mirror is presented in this paper. Secondly, the on-orbit stability of COCTS2 is evaluated. The results show that the bias of B16 compared with IASI is 0.14 K, with a standard deviation of 0.33 K. The bias of B17 and B18 with IASI is less than 0.1 K, with standard deviation of about 0.5 K. The Noise Equivalent Difference Temperature (NEDT) is less than 0.1 K for three bands. The temperature of two blackbodies, the digital number of the detector, and the NEDT remain stable.