Abstract: Ecological agriculture is the efficient approach and necessary choice for agriculture sustainable development in China, and ecological animal husbandry system is the key content of ecological agriculture. Taking Zhoukou village as an example,energy input-output analyses of Zhoukou ecological animal husbandry system is dealed with and the impact on the village animal husbandry system by biogas project is estimated. The estimated results indicate that biogasproject into ecological animal husbandry system can efficiently transform the waste produced during the agricultural production, realize the multilevel utilization of resources, establish substance positive circulation inside the system, improve the environment of rural area, and accelerate the coordinated development of economy, resource and ecological environment.