Harmonic gears are widely used in precise space technology, robotic, medical equipment and other fields, while the magnitude of surface topography changes due to wear is usually comparable to or larger than the original surface roughness and elastic deformation, leading to severe transmission failures. This paper reports a numerical approach to simulate the lubrication status considering wear evolution based on mixed elastohydrodynamic lubrication (EHL) and Archard models, in which the Reynolds equation is solved with finite difference method and surface deformation is calculated by the discrete convolution‐fast Fourier transform (DC‐FFT) algorithm. The interfacial pressure and film thickness distributions are validated by comparison with available results from literature. The harmonic gear lubrication and wear performances are calculated, including effects of machined surface, velocity, load, wear time and material properties, and the results suggest that avoiding long‐term and high‐torque working with a large wear coefficient can effectively prevent surface wear failure, which is beneficial for increasing the harmonic gears' lifespan.