Abstract: Biogas system is the pivot in material recycling and energy transformation of a complex agro-ecosystem.It takes agricultural organic waste materials as its raw material and produces high efficient,clean and multi-purposed fuel,forage and manure.The important roles of biogas system in the protection of rural eco-environment and in the improvement of eco-agriculture development are described in this paper.The problems existed in the development of biogas technology in China have been pointed out and the countermeasures for dealing with those problems have also been put forword.