Abstract: Through the application of ecological and systems theory, this paper investigated energy flow in cropland, orchard and animal husbandry subsystems of agro-ecosystem using 40 typical peasant households of Daxi Village, Yuli County, Southern Xinjiang as a study unit. Energy flow mechanism, supplemental energy input structure, energy input and output composition for different subsystems, energy flow relation among subsystems and energy transform efficiency were analyzed. The results show that peasant household ecosystem is a multi-operational system that is not only an essential traditional agriculture but also a modern agriculture. Due to low total supplemental and organic energy input in agricultural systems, utilization efficiency of solar energy and output levels are low. Increasing total supplemental and organic energy input can improve energy transformation efficiency, hence energy output levels. Energy relationship between primary and secondary production systems is in disharmony, with large energy deviation that not only results in serious organic energy waste (provided by primary production system), but equally brings about scarcity in the sources of organic fertilizer. Hence developing animal husbandry can be an effective and important way of optimizing peasant household production structure, coordinating relationships between cropping and breeding systems and increasing energy outputs.