Agricultural microbial germplasm resources are involved in all aspects of agricultural production and are crucial for ensuring food security, facilitating scientific and technological innovation, and promoting high-quality development of agriculture. Therefore, it is urgently needed to clarify the current status of the protection and utilization, identify existing problems and deficiencies, recognize the gap with resource-powerful countries, and clarify the key development directions of agricultural microbial germplasm resources in China. This study reviews the current situation of protection and utilization of agricultural microbial germplasm resources in China and abroad from the aspects of the protection and utilization system, agricultural scientific and technological innovation, and effectiveness of development and utilization. By comparing and analyzing international development trends, we reveal that China's agricultural microbial resources are currently in a stage of rapid development in terms of resource reserves, preservation facilities, utilization, and industrial support. However, compared with resource-powerful countries, China still faces significant challenges including poor infrastructure conditions, unclear inventory of resources, lagging precise identification and evaluation, and insufficient core germplasm. To address this, it is proposed to strengthen top-level design to make overall arrangement for the protection and utilization of agricultural microbial germplasm, enhance infrastructure construction by planning a project for improving resource preservation capacities, emphasize original innovation to establish a collaborative research model for the exploration of agricultural microbial resources, focus on demand-driven efforts to provide key support for the development of the agricultural microbial industry. These efforts aim to promote the protection and utilization of agricultural microbial germplasm resources in China and achieve high-quality agricultural development.