Metal roof systems were widely utilized in various important buildings; however, cases of wind damage were often observed. In this paper, wind uplift tests of standing seam aluminum magnesium manganese and continuous welded stainless-steel roof systems were conducted, and the wind resistance bearing capacity and mechanical properties of key joints in the two roof systems were compared and analyzed. Strain gauges and displacement sensors were arranged at different structural layers and key nodes of the roof system to compare and analyze the stress and displacement changes. The results showed that the wind resistance capacity of the continuous welded stainless-steel roof system was more than 25% higher than that of the standing seam aluminum magnesium manganese roof system. The stress and displacement of the roof system gradually increased with the increase in wind load. Obvious differences in stress at different positions of the two roof systems were identified. The stress at the roof panel of the roof system was greater than that of other structural layers, and the maximum displacement of the roof panel in the elastic stage could reach more than 97.5 mm. The fitting coefficient between the test and the finite element was 0.976, and the ultimate bearing capacity of Specimen B was 479.64 MPa. The research results of this paper can provide some data support and reference for engineering design and applications.