With the continuous expansion of the depth and breadth of technological research, technological innovation has shown the characteristics of cross-regional, cross-institution and multi-technology integration, and it has become difficult for a single region, a single institution and a single technological field to support complex and large-scale technological innovation. The collaborative innovation mode is based on the reasonable flow of innovation factors, which can form knowledge synergy and spillover effect, enhance innovation efficiency, and is an inevitable choice for regional technological innovation and achieving high-quality development. Currently, there remains a significant gap in scientific and technological innovation between the Chengdu-Chongqing area and the Yangtze River Delta. Achieving collaborative innovation is crucial to establishing a pivotal growth engine and new dynamic source that drives high-quality development nationwide. This also represents a key initiative to develop new quality productive forces tailored to local conditions and advance a new pattern of large-scale western development. Based on the theory of division of labor and technology evolution, this paper divides synergy innovation into three categories: technological synergy, institutional synergy and regional synergy. And based on patent information data, this paper analyzes the evolution characteristics of synergy innovation network in Chengdu-Chongqing area, and empirically analyzes the impact of three synergy models on the quantity and quality of regional innovation. Results show that: 1) Regional collaborative innovation in Chengdu-Chongqing area shows networking trend, but with core-periphery structure. Universities are the key nodes of the innovation network, and technology is highly related in the same industry.2) Technological synergy can improve the quantity of regional innovation through the effect of technological optimization and reorganization, but this path dependent development can inhibit the quality of innovation; institutional synergy and regional synergy can update the knowledge base through knowledge sharing and thus improve the quality of regional innovation. Based on this, this paper puts forward three suggestions: First, we should accelerate the technological innovation cooperation across administrative boundaries, continue to play the role of knowledge spillover in key node areas, accelerate the construction of science and innovation corridor, and strengthen the spatial spillover between the core node and sub-nodes of technological innovation. Second, promote technological collaboration with universities to advance industry-university-research integration. Improve the ownership system for scientific and technological achievements, promote technology exchanges and joint R&D between universities as well as between universities and enterprises, and drive the integrated development of technological innovation and industrial innovation. Third, it is necessary to carry out collaborative cultivation of related technologies, compile technology linkage tables, and increase inputs in technology fields that are urgently needed for industrial development and have a high degree of relevance, so as to achieve a shift from single technology innovation to collaborative development of technology clusters. The article analyzes the characteristics and problems of the current collaborative innovation network in Chengdu-Chongqing area, and empirically tests the positive effect of collaborative innovation on innovation output, which can provide a reference for local governments to optimize the regional innovation pattern.