The boundary layer fluid and its viscosity changeshave a significant impact on the flow of fluids in low permeability media. Existing low-velocity non-Darcy flow models usually ignore the change of fluid viscosity, or simply treat the fluid viscosity as a function of pore radius. The viscosity of boundary layer fluids is usually related to contact angle. In this paper, based on capillary model and fractal theory, a new low-velocity non-Darcy flow model is proposed considering the influence of contact angle on the viscosity of boundary layer fluid. The reliability of the model was verified through experiments and the sensitivity analysis of key parameters was conducted. The results show that the contact angle has a significant impact on the viscosity of the boundary layer fluid, which in turn affects the flow behavior of the fluid. After considering the change of fluid viscosity in the boundary layer, the flow velocity decreases. In this experiment, compared with ignoring the change of fluid viscosity, the decrease in flow velocity can reach 57.1%. The flow velocity decreases with the increase of fractal dimension of pore distribution (Df) and increases with the increase of contact angle. In this paper, under the same pressure gradient, when Df increases from 1.2 to 1.8, for every 0.2 increase, the flow velocity decreases by 18.4%, 23.3%, and 29.1%, respectively; When the contact angle increases from 0° to 80°, for every 20° increase, the flow velocity increases by 10.9%, 12.3%, 14.0%, and 16.3%, respectively. As the pressure gradient increases, the boundary layer fluid participates in the flow, and the effective seepage section and fluid effective viscosity increase. The increase of fluid viscosity has retarding effect on the flow, but the effect is smaller than the gain effect of the increase in flow section on the flow velocity. Therefore, in general, the flow velocity increases with the increase of the pressure gradient.