The rational allocation of urban-rural ecological resource is the internal requirement for the urban-rural integration. The low efficient allocation of urban-rural ecological resource can be showed in many aspects，such as the single way of exporting rural labor resources，the serious problem of rural environment，the rural natural resources are plundered by cities，the transformation of urban polluting companies to rural，and the shortage of rural public infrastructure. The deep crux of these problems is rooted in the losing regulation of the market and the government. To promote the rational allocation of urban-rural ecological resource，we should adhere to the eco-system orientation principle of taking humans as essentials，deepen the market cognition about ecological resource value，establish the information network platform of allocation of urban-rural ecological resource，improve the ecological compensation mechanism between urban and rural，play other dominant function of government.