<p>Existing studies on urban innovation networks predominantly focus on multidimensional proximities. To advance this field, this study highlights the analysis of cities’ latent capacities, specifically potential comparative advantages (PCAs), as its core contribution. We analyze how industry-technology synergies driven by PCAs reshape collaborative innovation networks in China’s intelligent net-connected new energy vehicle (NEV) industry. Integrating product space and knowledge space theories, we construct a dual-layer network framework based on patent applications and industrial enterprise statistics to examine cities’ latent capacities across 53 Chinese cities (2013–2022). Using the Temporal Exponential Random Graph Model (TERGM) to analyze network dynamics, we found that: (1) Innovation collaboration is significantly driven by the complementarity between one city’s latent technological potential and another’s existing industrial capabilities. This indicates that partnerships are formed not just by similarity, but by matching local potential with external expertise. (2) Core industry segments, such as batteries and intelligent systems, rely heavily on these cross-domain synergies. Additionally, supporting services, such as engineering research and charging services, play a foundational role in NEV industry chain development. (3) The innovation network demonstrated emergent small-world characteristics. However, the significant influence of PCA synergies indicates that cities are actively utilizing latent capacities to build cross-regional bridges. This mechanism suggests that the strategic alignment of regional PCAs can help transcend structural lock-ins, thereby disrupting path-dependent trajectories and increasing network adaptability. These findings extend proximity-centric frameworks by revealing how latent synergies work alongside traditional proximities and advance innovation network theory through evolutionary economic geography.</p>