It is of great theoretical and practical significance to optimize and improve the design of rural human settlement units through system ecology analysis based on emergy evaluation indices. From the perspective of system ecology, the rural living environment system is multivariate and complicated, with strong correlations and obscure boundaries between levels. Therefore, the definition of a rural human settlement unit in China is proposed in this research and can be divided into three scales: the microcosmic scale, mesoscale, and macroscopic scale. This research adopted a new method for the design of rural human settlement units by adopting emergy as a common dimension in order to solve the problem of dimensionality disunity between resource environment elements and society economy elements. Through the establishment of the static emergy analysis model and dynamic emergy prediction model, qualitative and quantitative analysis approaches of the rural human settlement unit were combined. According to the design orientations of industry-invigorative, environment-friendly, and ecology-balanced, corresponding with production-living-ecology integration, emergy evaluation indices including the emergy self-sufficiency ratio, emergy investment ratio, net emergy yield ratio, environmental load ratio, and emergy sustainable indices were calculated and predicted by means of system dynamics simulation. The dynamic emergy prediction results showed that the emergy self-sufficiency ratio and emergy sustainable indices basically presented a decreasing tendency, from 0.34 to 0.15 and from 0.76 to 0.57, respectively, with the passage of time; the values of the emergy investment ratio, net emergy yield ratio, and environmental load ratio basically presented an increasing tendency, from 2.13 to 2.78, from 1.66 to 2.12, and from 2.23 to 3.61, respectively, with the passage of time. In practice, the evaluation method based on the emergy analysis of the technical strategies and spatial arrangements of the rural human settlement unit can provide data support for designing standards, planning guidelines, and creating constructional instructions for the rural living environment of China.