High-temperature superconducting (HTS) magnetic bearings have great potential in the field of rotating machinery, such as flywheels and momentum wheels, because of their low friction and self-stabilizing capability. The study of rotational loss in HTS bearing is of great significance to achieve better efficiency. Previous research indicates that low rotational loss has a close relation with hysteresis loss in HTSs and eddy-current losses in the surrounding metal materials. A low coefficient of friction (<10−8) at low speed is attractive for high precision instruments. This paper first presents a short overview of low rotational loss in HTS bearings, and then a special design of HTS bearing is given for application in micro-thrust measurements of space propulsion. The load capacity of the bearing allows for up to 10 kg, which means that the entire thruster system can be suspended to avoid measuring the internal force. Two different measuring methods are designed to fit several operational modes of the micro-thruster, and the measured thrust level is from 1 mN to 100 mN. The bearing system shows great response to short pulse modes of the micro-thruster, and an impulse of 1 mN·s was identified accurately. The measured thrust shows great agreement with the designed values of the micro-thruster, indicating the effective application of the HTS bearing for micro-thrust measurements.