Based on the triple perspectives of “technology-organization-environment”, combining the characteristics of packaging companies to build a corresponding TOE framework, and using 2018 A-share listed packaging companies as the sample, a fuzzy set qualitative comparison analysis was conducted to explore the synergy and driving paths affecting the innovation performance differences of listed packaging companies. The results showed that under the triple linkage of technical factors, organizational factors and environmental factors, the listed companies in the packaging industry with high innovation performance presented two different modes, and three kinds of configuration paths producing non high innovation performance. By observing the configuration-substitution relationship producing high innovation performance, it was found that under certain conditions, there existed substitution relationship among technology, organization and environment. The company’s R&D capabilities and corporate governance power played an important role in promoting high innovation performance.