Shale oil reservoirs are characterized by low porosity, ultra-low permeability, and highly inhomogeneous. Additionally, shale reservoirs contain nano- and micro-nano-scale pores, as well as flow channels such as natural microfractures and artificial fractures. Different flow channels have diverse flow features and characterization difficulties, and conventional simulation and evaluation methods are inapplicable, which used methods posing challenges for the evaluation of shale reservoir production capacity accurately. This paper establishes a mathematical model of multiphase flow in porous media considering liquid–solid adsorption and wall slip effects in micro- and nano-constrained space as the initial step. Secondly, a comprehensive discrete fracture model is used to characterize microfractures and artificial fractures accurately, and a unique multi-scale seepage mechanism simulation method for shale reservoirs is developed. Finally, using this numerical simulation method, a capacity evaluation study is carried out for a target zone in the Gulong Shale reservoir by combining practical production data. This study analyses the influences on production potential based on the sensitivity of each mechanism and parameter. The results show that the confinement effect reduces the fluid bubble point pressure, and considering the confinement effect, the production capacity of the model is increased by 20%; Considering the activation pressure gradient and stress sensitive model, the production capacity decreases by 15% to 30%, which has an inhibitory effect on production capacity. The research results provide strong support for the production and production capacity prediction of the Gulong shale oil reservoir.