The two shortwave infrared (SWIR) bands (1.64 and 2.13 μm) of Medium Resolution Spectral Imager (MERSI) onboard FY-3B are detected by photovoltaic HgCdTe detectors. Due to the issue of radiant cooler, the SWIR band detectors operated at higher temperatures than specification, which influenced its on-orbit radiometric response. The long-term on-orbit radiometric properties of FY-3B MERSI SWIR bands at high working temperature were systematically studied. The time series of space view observation and telemetry temperature measurement were used to analyze the on-orbit temperature dependency. It revealed that there were positive correlations between the SWIR band space view and the detector temperature. Linear models were used to describe the temperature dependency and the temperature correction factors were derived. When the detector temperature changed 1℃, the space view digital number varied 0.7% and 5% for bands of 1.64 and 2.13 μm, respectively. After the temperature correction, the long-term variation of space view observations decreased significantly. The multi-site calibration method was used to obtain the on-orbit sensor radiometric response change. At the reference temperature, the total attenuations of 1.64 and 2.13 μm bands were about 6% and 11% respectively from Nov. 2011 to Dec. 2016. Through the cross comparison against Aqua moderate-resolution imaging spectroradiometer (MODIS), it revealed that when the daily calibration update model based on long-term trending analysis was applied, the radiometric differences between MERSI and MODIS were relatively stable for many years, regardless of whether the temperature effect was accounted for or not in the calibration process, which can meet the calibration expectation of 7%.