China’s national food security faces rigid constraints due to land scarcity, a large population, and heavy reliance on imported feed proteins. In this context, the initiative to seek calories and proteins from microbes has become a strategic priority for building a diversified food supply system. Microbial alternative proteins represent a quintessential new quality productive force in agriculture. They offer distinct advantages, most notably high industrial efficiency and the ability to decouple protein production from food crops and arable land. This paper reviews China’s progress in this sector based on global biomanufacturing trends. The discussion focuses on synthetic biology-driven strain engineering, gas fermentation, and industrial-scale production. Furthermore, the article critically analyzes current bottlenecks, including intellectual property barriers for elite strains, high production costs, and lagging safety evaluation standards. Finally, we propose targeted recommendations to address these challenges. These include strengthening organized basic research, establishing an intelligent manufacturing system that integrates education, technology, and talents, and reforming regulatory frameworks. These insights aim to provide a strategic reference for China to secure a commanding position in the global bio-agriculture landscape.