This paper investigates the potential factors contributing to reservoir damage in low permeability reservoirs, based on the micro-characteristics of pore throats. Through the utilization of numerical simulations, we investigate the micro-permeability behavior of fluids within these low permeability reservoirs. The simulations produce a micro-numerical field distribution of fluid within the reservoir (comprising velocity field, pressure field, and phase field), facilitating an analysis of evolving patterns and influencing mechanisms between oil and water phases during displacement processes. The simulation results indicate that with an increase in the number and diameter of plugged pores, there is a significant decrease in reservoir permeability. The permeability of pores smaller than 3.0 μm decreases to 92 % of the original value, while that of pores smaller than 3.5 μm drops to 87 %, and that of pores smaller than 5.0 μm decreases to 82 %. The rock stress sensitivity effect leads to a reduction in permeability, with a 94 % decrease when pore deformation reaches 95 %, and an 86.5 % decrease at a deformation level of 85 %. Leveraging these simulation results and considering potential formation damage that may occur during oil and gas field development processes, we propose targeted formation damage controlling measures to provide theoretical underpinning for efficient development strategies in low permeability reservoirs.