Discovered by Christopher Alexander, living structure is a physical phenomenon, through which the quality of the built environment or artifacts can be judged objectively. It has two distinguishing properties just like a tree: “Far more small things than large ones” across all scales from the smallest to the largest, and “more or less similar things” on each scale. As a physical phenomenon, and mathematical concept, living structure is essentially empirical, discovered and developed from miniscule observation in nature- and human-made things, and it affects our daily lives in some practical ways, such as where to put a table or a flower vase in a room, helping us to make beautiful things and environments. Living structure is not only empirical, but also philosophical and visionary, enabling us to see the world and space in more meaningful ways. This paper is intended to defend living structure as a physical phenomenon, and a mathematical concept, clarifying some common questions and misgivings surrounding Alexander’s design thoughts, such as the objective or structural nature of beauty, building styles advocated by Alexander, and mysterious nature of his concepts. For this purpose, we first illustrate living structure—essentially organized complexity, as advocated by the late Jane Jacobs (1916–2006)—that is governed by two fundamental laws (scaling law and Tobler’s law), and generated in some step by step fashion by two design principles (differentiation and adaptation) through the 15 structural properties. We then verify why living structure is primarily empirical, drawing evidence from Alexander’s own work, as well as our case studies applied to the Earth’s surface including cities, streets, and buildings, and two logos. Before reaching conclusions, we concentrate on the most mysterious part of Alexander’s work—the luminous ground or the hypothesized “I”—as a substance that pervasively exists everywhere, in space and matter including our bodies, in order to make better sense of living structure in our minds.