“Rural molecular” structure transformation from star-like aggregates of “village atoms” to networked chains in China

Understanding the spatiotemporal evolution of rural structures is critical to achieving global sustainable development. However, due to the lack of long-term, micro-scale data at the national scale, these dynamic changes remain insufficiently observed. Here, we innovatively introduce a molecular perspective that conceptualizes villages as “atoms” and village structures characterized by specific inter-village spatial connections as “rural molecular structures”. Inspired by isomer concepts in physics and chemistry, we quantify these structures using rural molecular potential energy as a topology-sensitive metric of inter-village organization. Analyzing 495,314 villages across 2465 Chinese counties during 2000–2020, we show that underdeveloped northwestern counties are dominated by star-like aggregates, where a few low- or mid-stage villages drive the growth of numerous distant secondary settlements under large urban–rural income gaps. In contrast, developed southeastern counties form modular networked chains, with mid- and high-stage villages sustaining dense, localized interactions and high systemic cohesion. Nationally, hierarchical distances expanded rapidly in 2000–2010 (≈2 km yr⁻¹ on average; ≈6 km yr⁻¹ between Stage 3 and Stage 2), but contracted in 2010–2020 (≈1 km yr⁻¹; Stage 3-Stage 2 ≈ 1 km yr⁻¹), indicating a shift from centrifugal expansion to centripetal consolidation. Furthermore, causal forest inference indicates that urban–rural integration increases rural molecular potential energy, facilitating factor circulation, weakening core monopolies, strengthening long-range complementarities over time, and steering lagging regions toward more networked configurations. By translating rural spatial organization into a scalable and topology-sensitive metric, our approach provides a quantitative basis for monitoring rural structural reconfiguration and refining adaptive governance and intervention strategies in a timely manner.