Feed-forward 3D foundation models face a key challenge: the quadratic computational cost introduced by global attention, which severely limits scalability as input length increases. Concurrent acceleration methods, such as token merging, operate at the token level. While they offer local savings, the required nearest-neighbor searches introduce undesirable overhead. Consequently, these techniques fail to tackle the fundamental issue of structural redundancy dominant in dense capture data. In this work, we introduce \textbf{S-VGGT}, a novel approach that addresses redundancy at the structural frame level, drastically shifting the optimization focus. We first leverage the initial features to build a dense scene graph, which characterizes structural scene redundancy and guides the subsequent scene partitioning. Using this graph, we softly assign frames to a small number of subscenes, guaranteeing balanced groups and smooth geometric transitions. The core innovation lies in designing the subscenes to share a common reference frame, establishing a parallel geometric bridge that enables independent and highly efficient processing without explicit geometric alignment. This structural reorganization provides strong intrinsic acceleration by cutting the global attention cost at its source. Crucially, S-VGGT is entirely orthogonal to token-level acceleration methods, allowing the two to be seamlessly combined for compounded speedups without compromising reconstruction fidelity. Code is available at https://github.com/Powertony102/S-VGGT.