Static uniform pressure tests are widely recommended to determine the ultimate capacities of standing seam roof systems in many building standards and guidelines, but such ultimate wind-resistant capacities are usually much different from those under dynamic non-uniform wind pressures. Through the comparison of the ultimate capacities of standing seam roof systems under static uniform pressures and dynamic non-uniform wind pressures by finite element simulations, the definition and calculation steps of influence coefficients of dynamic non-uniform wind pressure distribution (ICDNWPD) are proposed to reflect the effects of actual wind pressure distributions on wind-resistant capacities of the roof cladding systems. The effects of roof zones, support spacings, and terrain categories on the ICDNWPDs of flat roofs are investigated. The results show that the ICDNWPDs of the edge and interior regions are approximately 1.27–1.42 times those of the corner zones, and the ICDNWPDs are more sensitive to the roof zone than the support spacings and terrain categories. The factors of safety of roof systems with larger spans or under smoother terrain or located in the roof corner zone should be greater, which cannot remain constant.