Due to the high-efficiency energy absorption and high-tension strength material properties of spider silk, many researchers have studied the mechanical properties and microstructure of the spider web. The concept of spider web structure has been recognized to be adopted for structural engineering aspect. The structure of spider web and its material properties have been studied for decades. However, the fundamental free vibration mode shapes and their corresponding frequencies have never been fully investigated. This study investigates the nonlinear characteristics in the large-amplitude free vibration of imperfect spider web structures using finite element analysis. The spider web applies the concept of elastic cables taking only axial deformation into account. The finite element models of a spider web considering geometric nonlinearities are employed. It should be noted that spider web could experience large deformation when the spider uses its silk to catch prey. This research aims at analyzing the linear and geometric nonlinear behaviour of imperfect spider web structure. Four different types of imperfect spider web: spiral imperfect spider web, radial imperfect spider web, central imperfect spider web, and circular rings imperfect spider web, are considered. It is found that pretension in spider silk plays a significant role in nonlinear vibration characteristics of the spider web. Moreover, the radial thread damaged tends to have a greater effect on structural free vibration of spider web in comparison with other imperfections. The outcome will help a structural engineer to adapt the concept of spider web, its properties, and damage patterns for any larger structures.