The present paper proposes a measure for improving the wind-resistant performance of photovoltaic systems and mechanically attached single-ply membrane roofing systems installed on flat roofs by combining them together. Mechanically attached single-ply membrane roofing systems are often used in Japan. These roofing systems are often damaged by strong winds, because they are very sensitive to wind action. Recently, photovoltaic (PV) systems placed on flat roofs have become popular. They are also often damaged by strong winds directed onto the underside, which cause large wind forces onto the PV panels. For improving the wind resistance of these systems, we proposed to install PV panels horizontally with gaps between them. Such an installation may decrease the wind forces on the PV panels due to the pressure equalization effect as well as on the waterproofing membrane due to the shielding effect of the PV panels. This paper discusses the validity of such an idea. The pressure on the bottom surface of a PV panel, called the “layer pressure” here, was evaluated by a numerical simulation based on the unsteady Bernoulli equation. In the simulation, the time history of the external pressure coefficients, measured at many points on the roof in a wind tunnel, was employed. It was found that the wind forces, both on the PV panels and on the roofing system, were significantly reduced. The reduction was large near the roof’s corner, where large suction pressures were induced in oblique winds. Thus, the proposed method improved the wind resistance of both systems significantly.