As vehicles for implementing innovation-driven strategies, the strategic emerging industries are crucial for enhancing national competitiveness and sustainable development. Improving innovation performance in these industries has been a central focus of academic research. Notably, existing studies have primarily analyzed the net effects from a single perspective. This study examined 261 strategic emerging Chinese enterprises listed on the A-share market. Utilizing the Technology–Organization–Environment framework and fuzzy set qualitative comparative analysis, this study explores the impact paths and mechanisms of the coupling configurations of technology, organization, and environment to enhance enterprises’ innovation performance from a configuration perspective. We discovered that, first, no single antecedent condition is necessary to achieve high enterprise innovation performance. However, increasing the level of digital transformation and intensity of innovation investments universally results in high innovation performance. Second, the technological, organizational, and environmental conditions exhibit “multiple concurrency”, forming diverse configurations that drive enterprise innovation performance; hence, the driving paths of enterprise innovation performance are varied. Third, four schemes exist for achieving high innovation performance in strategic emerging enterprises: environment-driven under technological dominance, technology–organization driven type, organization-driven under technological–environmental dominance, and technology–organization–environment co-driven type. Exploring the synergistic paths driving innovation performance from a configuration perspective enhances our understanding of the complex interactions among multiple factors in improving such performance. This provides significant theoretical and practical implications for enterprises aiming to improve their innovation performance.