The spatial configuration and collaborative networks of research and development (R&D) enterprises are continuously reshaping the innovation landscape of strategic industries. Clarifying this evolution is crucial for advancing China’s lithium-ion battery (LIB) sector. Leveraging a unique dataset of corporate LIB patents, this study examines the co-evolution of spatial agglomeration and inter-city collaborative networks within China’s LIB industry. Integrating spatial statistics, social network analysis, and geographic detectors across four sub-periods, we systematically track this reshaping process and identify its driving forces. Our findings reveal a dual trajectory of restructuring. Spatially, LIB R&D enterprises exhibit persistent east-west disparities, with innovation hotspots concentrated in coastal urban clusters, the Yangtze River Delta, Pearl River Delta, and Beijing-Tianjin-Hebei region. However, standard deviation ellipse analysis indicates a significant northward shift in the distribution center toward Ji’an, Jiangxi Province, suggesting gradual restructuring toward inland regions. In the network dimension, inter-city collaboration has expanded from 2 to 157 cities, yet overall connectivity remains low and fragmented. Notably, high-level connections concentrate among core cities unconstrained by geographical distance, indicating network structure is reshaped by node hierarchy rather than spatial proximity. Further analysis reveals that regional economic openness, industrial agglomeration, technological innovation capabilities, and policy support collectively shape enterprise distribution and network positions. By integrating spatial and network perspectives, these findings advance understanding of how strategic industries reshape regional innovation landscapes and provide evidence-based implications for fostering a more balanced and connected technological innovation landscape in China.