The university-anchored innovation and entrepreneurship ecosystem serves as both a spatial carrier and an institutional innovation that promotes science-education integration and facilitates the commercialization of scientific and technological achievements. Based on the innovation ecosystem theory and the triple helix theory, this article constructs a four-dimensional analysis framework from the perspective of science and education integration - “disciplinary collaboration, resource integration, talent connection, and achievement commercialization,” and conducts a systematic investigation of the innovation and entrepreneurship ecosystem anchored by ten universities in Chongqing. The study found that Chongqing’s ecosystem construction has evolved from space carrier development to innovative ecosystem cultivation, forming a local practice model of “university-local government collaboration, full-chain empowerment, and precise peer-based incubation.” However, there are still obvious bottlenecks in terms of the depth of disciplinary collaboration, the efficiency of resource integration, the talent connection mechanism, and the effectiveness of commercialization of results. This article proposes that Chongqing should transition from the “factor aggregation” stage to the “ecological symbiosis” stage. By optimizing top-level design, improving platform construction, strengthening technological empowerment, and improving the service ecosystem, a university-anchored innovation and entrepreneurship ecosystem construction plan with Chongqing characteristics can be formulated to provide replicable and scalable experience for similar cities.