Environmental problems are closely related to society's processing of materials through the entire economy. Because neither traditional environmental nor economic analytical methods can provide sufficient insight into the physical dimension of economies, this article presents an integrated methodology, combining a substance flow analysis (SFA) approach and an ecological restructuring analysis. This approach is applied to phosphorus (P) in China, one of the most rapidly growing industrializing economies, in order to better understand of the economy's material use and its change over time. A static national SFA model is developed with statistical data from 1996. By tracking the national economy's P flows from origins to destinations, the critical P flows with respect to environmental impacts are identified. Based on the regime of national P flows, this article analyzes the degree of ecological restructuring by dynamically describing the structural changes of related critical P flows over the last two decades with a set of ecological restructuring indicators (ERIs). Finally, some potential and desired changes are discussed, with the goal of ecologizing the national P flow regime; that is, reducing the ecological impact of the national P flow regime. The methodology of this article illustrates its applicability and value for presenting an overall insight into the physical dimensions of national economies.