As a strategic emerging industry, the nuclear technology application sector is characterized by high technology, high efficiency, and high quality. Promoting the innovation and development of nuclear technology application is an inevitable choice in response to the new round of scientific and technological revolution as well as industrial transformation. It also represents the optimal direction for expanding the application fields of nuclear technologies, fostering high-quality development of the sector, and cultivating new productive forces. This study examines the deep integration of scientific and technological innovation with industrial innovation. It summarizes the essence and key characteristics of deep integration of scientific and technological innovation with industrial innovation in nuclear technology applications. It analyzes the diverse innovation entities and innovative integration mechanisms within nuclear technology applications, proposing a systematic framework for innovative integration in this field. Building on this foundation, it examines the current status and challenges facing the innovative integration, and proposes the following targeted policy recommendations: (1) improving the overarching planning and regulatory standards for the nuclear technology application industry, (2) enhancing the supply of high-quality scientific and technological resources for nuclear technology application, (3) strengthening the foundational infrastructure for the nuclear technology application industry, and (4) promoting the high-quality transformation of nuclear technology application outcomes. These recommendations provide theoretical support and practical guidance for driving the high-quality development of the nuclear technology application industry.