“Fragmented” cultivated land governance conforms to the inherent requirements of high-quality development, and responds to the strictest requirements of cultivated land protection dimension in the new development stage. This paper focuses on the problem of “fragmented” cultivated land that modern agriculture must face, tries to analyze the endogenous logic and practical challenges faced by the governance of “fragmented” cultivated land under the background of high-quality development from different dimensions, and focuses on the overall resource space optimization, promote the fragmented continuous improvement, improve the incentive mechanism, empower the ecological culture and other aspects of targeted suggestions. The results show that, although “fragmented” cultivated land governance is a long-term process, orderly promotion of “fragmented” cultivated land governance will largely play an effective role in promoting the “trinity” protection of cultivated land quantity, quality and ecology, improving the utilization level of cultivated land capacity, promoting large-scale governance of cultivated land, guiding the optimization of spatial resources, and promoting ecological services of cultivated land. In the process of orderly cultivation of “fragmented” cultivated land and improving the quality of existing cultivated land, strict control over the use of cultivated land will be implemented, and centralized and contiguous protection and quality improvement of cultivated land will be promoted with the goal of improving the protection of cultivated land by agglomeration. The research results are expected to provide useful theoretical reference and decision-making reference for further promoting the governance of “fragmented” cultivated land.