China's grain production has transformed from absolute shortage to a current structural oversupply. High-intensity production introduced further challenges for the eco-environment, smallholder livelihood, and the man-land interrelationship. Driven by urban-rural transformation, research on food security patterns and grain production has expanded into a new field. To analyze the challenges and required countermeasures for China's grain production system (GPS), this study constructed a theoretical GPS framework based on space resilience. Firstly, a new GPS concept was proposed and a functional system was established for protecting the regional food security, thus guaranteeing smallholder livelihood, stabilizing urban-rural transformation, and sustaining the eco-environment in terms of economic, social, and ecological attributes of the GPS. Secondly, based on a cross-scale interaction analysis that varied from a smallholder scale to a global scale, the systematic crisis of the GPS was analyzed. Thirdly, a cross-scale analytic framework of the GPS was formed from the perspective of spatial resilience, integrating both inner and external disturbance factors of the GPS. Both spatial heterogeneity and connectivity of internal and external disturbance factors are important contents of system space resilience. Finally, the hierarchy of spatial resilience of GPS became clear. The transformation of labor force and the land use transition form key thresholds of the GPS. In summary: based on protecting the basic functions of the GPS, the cross-scale effect of systematic disturbance factors and relevant countermeasures for spatial resilience are effectively influenced by the coordination of the interests of multiple stakeholders; spatial resilience is an effective analytical tool for GPS regulation, providing a reference for revealing the inherent mechanism and functional evolution of the GPS in the process of urban-rural transformation.