The main factor contributing to the decline in effective fracture width and conductivity is proppant embedding into the fracture surface. In the deep shale's high-temperature, high-pressure, and high-stress environment, the rheological properties of rock cause proppant embedding to be deeper. Additionally, the effect of hydraulic fracture is difficult to maintain after fracturing, which causes a sharp decline in cumulative production. In this paper, the Hertz contact theory is used to establish a long-term fracture conductivity model that incorporates the two embedding behaviors of proppant elastic deformation and reservoir creep deformation. Through time integration, the variation of long-term fracture conductivity is obtained. The experimental data and the theoretical model agree well. The results show that long-term fracture conductivity gradually decreases as the proppant progresses from the elastic embedding stage to the creep embedding stage. The elastic modulus, viscoelastic coefficient, and particle size significantly impact on the fracture width. The rock's elastic modulus and viscoelastic coefficient have a negligible impact on the long-term fracture conductivity, which is positively correlated with sand concentration, proppant particle size, and elastic modulus. In this research, an accurate and effective analysis model is proposed to quantify the long-term fracture conductivity, reveal the hydraulic fracture closure mechanism of deep shale under high temperature and high stress, and provide technological solutions for long-term maintenance of high conductivity fracture channels, which is useful to increase deep shale production efficiency, lower the production decline rate, and extend the stable production cycle.