Metal roof systems are widely used in various landmark buildings. Understanding the natural vibration characteristics and primary influence of the roof system is useful for improving the roof system’s service life and maintaining the project’s safety. In addition, it is helpful to analyze the vibration force of the structure under earthquake and wind load. In this paper, the experimental investigation of the natural vibration characteristics (NVC) of two commonly used structural forms of standing-seam metal roof systems is carried out, and the influence of different boundary conditions, specimen width, panel width, and other parameters on the NVC are considered. The influence of different factors on the NVC of the roof system is analyzed in detail, and the main influencing factors and secondary influencing factors are studied. The research results show apparent differences in the NVC of the side and middle span of the roof panel under different parameters. The structural form has the most significant influence on the NVC of the roof panel, and the maximum influence on the peak acceleration (PA) and the fundamental frequency (FF) of the roof panel are 83.7% and 60%, respectively. The width of the specimen has a minor influence on the FF of the roof panel, and the minimum influence range is 6.9%. The influence of structural form, constraint form, specimen width, and panel width on the PA of the roof panel is far more significant than it is on the FF, with the difference between the two reaching 44.2%.