With the application of Big Data (BD), human production activities have been greatly affected, especially in the protection of environmental pollution in some regions. Therefore, the problems existing between the ecological environment and social and economic development should be paid attention to and solved in combination with the rapid development of science and technology. At present, the form is in the period of accelerated urbanization, industrialization and industrial structure adjustment. Due to the continuous improvement of urbanization construction speed, the coordination and unification of urban and rural planning has become one of the current research hotspots. There is a large amount of industrial wastewater and living garbage accumulation in rural areas, which seriously limits the application of BD technology. How to use scientific and reasonable methods to deal with it is extremely urgent. The traditional urban and rural natural environment protection model is too dependent on the professional opinions and subjective judgments of experts and scholars in the process of governance, and can not find the potential pollution in the natural environment in time. The means to deal with the environmental pollution problems are relatively simple. The cost of environmental protection is too high, and the implementation of natural environmental protection measures is not in place. To solve these problems, this paper proposed a model of urban and rural natural environment protection based on BD technology and combined with decision algorithm and computer technology. Through experimental comparative analysis, the innovative urban and rural natural environmental protection model was compared with the traditional urban and rural natural environmental protection model, and the average performance improvement was 13.8% in four aspects.