Advanced equipment manufacturing (AEM) is the core battleground for cultivating new-quality productivity. Addressing technological hollowing out and geographical lock-in in key areas, this paper constructs an embedded framework of “structural constraints and proactive choices” grounded in structured theory to clarify the micro-dynamics of cross-regional innovation network evolution, focusing on how innovation entities break through geographical lock-in. Using patent cooperation data from China’s high-end equipment manufacturing industry from 2013 to 2024, the study employs an exponential random graph model (ERGM) to analyze the following findings: First, structural constraints formed by multidimensional proximity exhibit significant endogenous dependence, but the network as a whole is undergoing a paradigm shift from local closure to breaking through structural constraints, achieving a leap from path dependence to path creation. Second, proactive choices based on capability complementarity, institutional compatibility, and relationship commitment (3C logic) are the core driving force for cross-regional alliances, effectively offsetting the transaction costs and uncertainties of remote cooperation. Third, technological capabilities have a significant proactive dissipation effect on geographical barriers, driving the network’s transformation from proximity-driven to capability-driven through a negative interaction with geographical distance. This research reveals the systemic logic of innovation entities breaking through geographical lock-in, providing a decision-making basis for improving the governance system of cross-regional collaborative innovation and solving bottleneck problems.