Rural communities can be conceptualized as spatial organisms interconnected by optimized resource utilization systems. Investigating the efficient utilization of rural resources and spatial construction methods grounded in resource metabolism is a pivotal step toward achieving the ecological transformation of rural spaces. This paper examined rural settlements in the Shandong Plain as a case study, exploring the relationships among three scales: village, neighborhoods, and courtyards. This analysis was based on elucidating the interaction mechanisms between “space and resource” and the integration of key resources and spatial elements. From the perspective of resource circulation and metabolism, this study aimed to elucidate the equilibrium of each resource element within three resource metabolism subsystems: the agricultural production system (core element), the ecological technology system (technological link), and the human life system (spatial carrier) in Shandong Plain’s villages, considering general climatic conditions. To achieve this, this research utilized the resource production volume, the utilization and transformation volume of resource metabolism technology facilities per unit area, and the average per capita resource consumption as fundamental measurement units. The concept of a rationing relationship is introduced to clarify resource allocation. Combining the aforementioned research on spatial resource metabolism in ecological villages in Shandong Province with the material flow analysis method, this study constructed a bottom–up spatial model of resource metabolism at three scales, courtyards, neighborhoods, and villages, under various resource metabolism scenarios. This study is anticipated to significantly contribute to the theoretical understanding of rural habitat environments, offering novel methods and perspectives for constructing ecological rural settlements.