The microbial industry, a key component of the strategic emerging sector of genetic technology, is vital for fostering new growth drivers and building global competitive advantages in China. With the world’s leading number of patent applications for deposited microorganisms, challenges in intellectual property protection arise due to their living nature and technical complexity, including safety compliance, novelty assessment, inventiveness evaluation, and sufficient disclosure in specifications. Based on China’s patent legal framework and practical cases, this study proposes strategies for cross-regulatory safety assessment, prior art evaluation, inventiveness through technical effects, and genetic resource disclosure. These provide standardized guidance for examiners and assist applicants in optimizing patent strategies, promoting the transformation of high-value patents and driving innovation in the microbial industry.