At present, the traditional progressive cavity motor is usually a rubber stator and metal rotor, and an interference fit is set. When it encounters the high-temperature formation of 180 °C and above, the carbonization of the rubber stator causes motor failure. Therefore, the all-metal progressive cavity motor adopts a metal stator and metal rotor, and the clearance fit is installed, which has good high temperature and corrosion resistance. The leakage caused by the clearance fit is the main reason for its performance output loss. Therefore, this paper is based on the leakage mechanism of all-metal progressive cavity motor and relies on the Couette flow, Poiseuille flow, and Bernoulli's theorem. Then the mathematical model of leakage and output performance of ∅95mm all-metal progressive cavity motor is established in this paper. The 3D-surface nephogram of the model about the effects of differential pressure, density, viscosity, and clearance on motor leakage was calculated numerically and iteratively by Matlab software. At the same time, through the calculation of the motor power loss of the structure design in this paper, the power loss is smaller in the clearance range, which provides a reference for the clearance selection of this kind of motor manufacturing. Finally, according to the mathematical model of the optimal clearance of 0.3 mm in the actual working conditions, the performance curve of the numerical calculation of the motor is demonstrated through the fluid simulation. Then the performance curve is compared and verified by the experiment of the InFocus company, which provides theoretical guidance for reducing leakage of motor and improving output performance.