Objective To explore the clinical application and effect of infrared thermal imager in blood flow monitoring after skin flap surgery by comparing with skin-contact thermometer. Methods Fifty patients who had undergone flap repair in the microsurgery ward of Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine between October 2019 and October 2020 were enrolled. An infrared thermal imager (FLIR ONE Pro) and a skin-contact thermometer were applied to monitor the skin temperature change till 7 d after surgery. The time consumed of using infrared thermal imager and skin-contact thermometer by different nurses, the efficacy of flap temperature monitoring of the two devices, the temperatures at different time points by using the two devices, and the temperatures under different distances to the flaps by using infrared thermal imager were compared. Results Different nurses had no difference in operating either of the two devices (P>0.05). It took significantly less time to measure the temperature of the flap area with the infrared thermal imager than using skin-contact thermometer [(39.28±3.52) vs. (103.85±9.09) s, P<0.001]. The skin temperature measured by the infrared thermal imager was significantly higher than that by the skin-contact thermometer (P<0.001), and the skin temperature measured by the infrared thermal imager at a height of 30 cm was higher than that at a height of 50 cm (P=0.006), but the temperature change amplitudes were both stable. Conclusions Infrared thermal imager is superior to skin-contact thermometer in terms of temperature measurement time, ease of operation, and sensitivity to temperature changes after skin flap operations. The thermal image collected by infrared thermal imager can provide an important basis for the identification of flap vascular crisis. It is a visual and objective blood supply monitoring equipment.