Driven by energy transition as well as the carbon peaking and carbon neutralization goals, China has basically established the pathway for developing a new energy industry system dominated by wind and solar power. Conducting research on the secure development of China's new energy industry system can help address the multidimensional and complex risks posed by the integration of a high proportion of renewable energy sources, thus providing crucial support for advancing the construction of this new energy system. This study analyzes the development characteristics and security landscape of China's new energy industry system, and identifies challenges it faces in areas such as supply chain resilience, core technology independence, standardization systems, and governance mechanisms. Based on this, a strategic framework for the secure development of the new energy industry system, centered around resilience‒flexibility synergy, is proposed. The study then clarifies strategic objectives for phased implementation, and outlines key tasks regarding industrial chain security, technological self-reliance, power system resilience, and digital-intelligent regulation, along with mid- to long-term engineering and technological support projects. Furthermore, the study offers policy recommendations from perspectives such as strategic coordination, deep integration of four chains (i.e., innovation, industry, capital, and talent chains), and digital-intelligent empowerment, thereby providing theoretical insights and decision-making support for building a secure, resilient, and efficient new energy system.