As one of the main numerical methods, the boundary element method boasts the advantages of fast computation speed and high accuracy. Based on the considerations of the influence of pressure drop, perforation height, skin coefficient, reservoir coefficient, and reservoir radius on the seepage law, a novel three-dimensional seepage model for vertical wells was established using the Laplace transform method and Stehfest numerical inversion method. The model was utilized to examine the velocity of pressure propagation and drop amplitude, revealing that the near-well area experienced faster propagation and drop than the far-well area. During dimensional analysis, it was observed that neglecting the effects of formation pressure change could lead to a substantial increase in the dimensional error of bottom hole pressure, with a maximum error of 9.45% recorded in this study. Additionally, a sensitivity analysis was conducted on perforation length, wellbore reservoir coefficient, skin coefficient, and reservoir radius to further elucidate the seepage law of vertical wells. This study provides theoretical guidance for oil and gas production. The original contribution of this research lies in the incorporation of formation pressure changes into the three-dimensional seepage model of vertical wells for the first time, which significantly enhances the model’s accuracy and practicality.