Abstract: As a strategic emerging industry in China, the Low-altitude economy is becoming a key area for cultivating new quality productive forces. With its high technological intensity, cross-industry integration, and strong potential for value creation, this sector is expected to reshape industrial structures and foster new modes of economic growth. Unlike traditional industries that rely on technology introduction and incremental absorption, the Low-altitude economy is distinguished by more pronounced innovation capabilities, thereby accelerating industrial modernization in China. Nevertheless, it also faces significant challenges, including technological immaturity, regulatory uncertainty, and high environmental risks. Against this backdrop, breakthrough innovation is not only essential for securing competitive advantages in global markets but also a key driver of high-quality and sustainable development. However, existing research at the micro-level remains limited, particularly on enterprise innovation strategies, organizational conditions, and their interaction with external environments. To bridge this gap, this study examines the diverse pathways through which breakthrough innovation occurs in the Low-altitude economy, demonstrates its pivotal role in advancing high-quality development, and provides both theoretical contributions and practical implications. Based on the TOE framework, this paper develops a complex mediation model that integrates QCA with regression analysis to systematically examine the pathways leading to breakthrough innovation and the mechanism of high-quality development in Low-altitude economy enterprises. This integrative approach provides a more comprehensive understanding of how technological, organizational, and environmental factors interact to generate innovation outcomes and foster sustainable development. The research findings are as follows: (1) The formation of breakthrough innovation capabilities follows multiple concurrent causal logics, and there is no single necessary condition. (2) There are five driving paradigms for enterprise innovation: R&D-driven, digital-driven, environment-driven, collaborative-driven, and innovation-trial-and-error-driven. (3) The complex mediation test shows that, except for the innovation-trial-and-error-driven paradigm, the other four paradigms can basically promote the high-quality development of enterprises through breakthrough innovation capabilities. These results not only deepen the understanding of how breakthrough innovation emerges but also indicate its pivotal role in promoting high-quality development. Beyond the key findings, this study contributes to the literature in several important ways. First, it shifts the analytical focus on the Low-altitude economy from macro-level regional governance to micro-level enterprise strategies, emphasizing how firm-specific technological, organizational, and environmental conditions shape innovation models and development paths. Second, from a methodological perspective, the integration of QCA with regression analysis offers a more nuanced understanding of causal complexity and provides novel insights for the study of complex systems. Third, the study extends the applicability of the TOE framework to dynamic and uncertain industrial contexts, while the identification of multiple effective innovation paradigms underscores the theoretical importance of strategic flexibility in enterprise innovation. From a practical standpoint, the study also offers actionable implications for both enterprises and policymakers. For enterprises, the findings suggest the need to carefully assess technological assets, organizational readiness, and environmental conditions before selecting appropriate innovation paradigms and development strategies. For policymakers, the results highlight the importance of targeted infrastructure investment, improvements in the business environment, and the development of supportive digital platforms to foster enterprise innovation and high-quality growth.