Abstract: A dog-breeding farmer household in northern Sichuan was used as a case to analyze and design an ecological farm household based on energy flow theory. The energy input-output of original ecological farmer household systems in 2008 was initially analyzed and diagnosed for ecosystem structures and benefits. According to the analysis results, two new design modes of farmer household ecosystems modeled with dog-breeding were proposed. Comprehensive input-output energy and benefits were comparatively analyzed, simulated and compared with the original system. The results showed that although the original ecological farmer household system was an organic ecosystem, its energy conversion rates and output capacity were very low. The ratios of solar energy and average energy input-output of both planting and breeding subsystems along with the energy cycle index of the original ecological farmer household system were 0.62%, 3.93, 0.32 and 0.70, respectively. This indicated lower organic energy input and suggested necessary improvements in energy flows. Compared with the original ecosystem, the two new designed ecosystems showed higher self-sustainability capacity and energy conversion efficiency. The ratios of solar energy and average energy input-output of both planting and breeding subsystems and the energy cycle indices of the new designed ecosystem modes 1 and 2 were 1.02% and 1.13%, 4.80 and 4.93, 0.48 and 0.46, 0.83 and 0.84, respectively. The comprehensive benefits of the designed mode 1 were higher than those of mode 2. The above analyses and results suggested that the study presented a very rigorous design of ecological farmer household. The results also contributed to developing new optimized design methods for farmer household ecosystems based on energy flow simulations and comprehensive benefit comparisons. More specifically, the analysis and design method of ecological farmer household in this study provided a realistic reference base for improving ecosystem energy output and benefit optimization.