It is a basic requirement of eco-garden city construction to establish a biodiversity protection system,and also a concrete requirement of ecological development for an eco-garden city.Biodiversity protection system of the eco-garden city includes the following contents:clarifying hierarchical requirements of the urban biodiversity protection,that is,classified protection of planning hierarchy and biodiversity hierarchy;achieving biodiversity protection via the planning system;establishing a quantity index system of urban biodiversity protection.Major strategies for establishing the biodiversity protection system were given as below:giving proper ecological planning and design;providing policy and law support;enhancing the construction of humanistic and education environment.Study on biodiversity protection system in eco-garden city may become an important support for the future quality evaluation of urban construction.