The environmental pollution caused by chemical elements not only exerts adverse impact on agricultural production and livestock and poultry raising, but also endangers the health of the human beings, which must be taken seriously. It is of great practical significance to study the environmental pollution caused by chemical elements. Based on the computer model method, this paper uses nitrogen as an example to establish a model of pollution process simulation and study the environmental pollution caused by chemical elements and the control methods. The results show that the environmental pollution caused by nitrogen can be divided into natural sources and human sources. For the Yellow River Basin, the biggest source of pollution is rural life and the application of nitrogen fertilizers; the export coefficient of applied nitrogen fertilizer is the highest while the export coefficient of soli nitrogen pool is the lowest; the key control period of different pollution sources in the Yellow River Basin is different and the key control period of natural sources is the rainy season while the key control period of human sources is the emission period. The control effect of reducing pollution sources of equal quantity on environmental quality is different. When the pollution source is reduced by 40% and 60% respectively, the most significant response of river nitrogen concentration is the atmospheric sedimentation. The research results provide a scientific theoretical basis and effective countermeasures for the treatment of environmental pollution caused by chemical elements.