In this study, the causality of climate and soil factors affecting the whole crop rye yield was identified via structural equation model, such as the seasonal effect between autumn and next spring, the indirect effect of the precipitation and the relationship between soil physical and climate factors. To identify the causality under the part of natural ecosystem, the structure was modeled with climates (autumnal accumulated temperature, autumnal growing days, spring accumulated temperature, spring growing days, spring amount of precipitation, and spring days with precipitation) and soil physical properties (drainage classes, effective soil depth, slope, and gravel content). As a result, we could estimate various specific relationships: First, the seasonal effect of accumulated temperature and growing days between autumn and next spring was obvious for the yield. Second, the precipitation had indirectly influenced the yield through suitable temperature in next spring. Final, the soil physical factor was related to the only precipitation, which means the effect of soil factor was significant through the spring precipitation. The structure could be modeled with climate and soil physical factors as a part of natural ecosystem, which was performed at the first time in the Republic of Korea and will be helpful to extend the structure with various factors in the future study.