In this paper, considering the specific business of Municipal Agricultural Economic Committee, we proposed a GIS-based system construction scheme based on the current situation and requirements of Qiqihar protected agriculture. Through its successful implementation, scientific monitoring and layout, guiding of scientific decision-making and timely macro-control can be provided for protected agricultural in Qiqihar. It will be convenient for the government to adjust the industrial structure of the regional agriculture efficiently and timely. It will help to overcome market failures and decrease the destruction of ecological environment caused by the traditional growth mode of agriculture. It can improve the level, quality and added-value of agricultural productions and save a lot of resource at the same.