In order to realize the thrust estimation of the Hall thruster during its flight mission, this study establishes an estimation method based on measurement of the Hall drift current. In this method, the Hall drift current is calculated from an inverse magnetostatic problem, which is formulated according to its induced magnetic flux density detected by sensors, and then the thrust is estimated by multiplying the Hall drift current with the characteristic magnetic flux density of the thruster itself. In addition, a three-wire torsion pendulum micro-thrust measurement system is utilized to verify the estimate values obtained from the proposed method. The errors were found to be less than 8% when the discharge voltage ranged from 250 V to 350 V and the anode flow rate ranged from 30 sccm to 50 sccm, indicating the possibility that the proposed thrust estimate method could be practically applied. Moreover, the measurement accuracy of the magnetic flux density is suggested to be lower than 0.015 mT and improvement on the inverse problem solution is required in the future.