Network represents adjacent relationships, connections, and interactions among constituent elements in complex systems but often loses critical information about spatial configurations. However, structure–function relationships in biological systems, e.g., the human heart, are highly dependent on both connectivity relationships and geometric details. Therefore, this paper presents a new self-organizing approach to derive the geometric structure from a network representation of the heart. We propose to simulate the network as a physical system, where nodes are treated as charged particles and edges as springs and then let these nodes self-organize to reconstruct geometric details. Despite random initiations, this network evolves into a steady topology when its energy is minimized. This study addresses the open question, i.e., “whether a network representation can effectively resemble spatial geometry of a biological system,” thereby paving a stepstone to leverage network theory to investigate disease-altered biological functions.