Intense, largely uncontrolled human activities (e.g., population growth, agricultural production, industrial development, energy consumption) have negatively affected urban and regional ecosystems. Nitrogen is an essential element for all ecosystems, and nitrogen export has been a major indicator of global change. However, quantitative assessment of the anthropogenic disturbance of the nitrogen cycle is still a challenge. A framework is proposed herein with respect to anthropogenic-derived nitrogen emissions in order to evaluate the ecological risk to urban and agricultural systems. An ecological risk is defined as the probability that a specific population, landscape, or ecosystem in a dangerous environment, will be negatively affected in terms of its health, productivity, hereditary features, or economic and aesthetic values. Chinese Taiwan's unique environmental background (i.e., intense agriculture, concentrated industry, numerous traffic facilities, and dense human population) make it ideal for this type of examination. The major human activities there have been considered in the assessment, including the daily activities of the population (e.g., industrial production, transportation, crop plantation, raising of livestock and poultry, aquaculture). Nitrogen emissions from human activities have affected the soil, water, and air in the local environment; therefore, the estimation of nitrogen exports integrated three major ecological risk sources. The degree of vulnerability for risk depends on the characteristics of the land use types, which are directly linked with urban planning. In this paper, land use types were classified as building areas, industrial areas, cultivated areas, forest lands, conservation areas, scenic areas, infrastructure, and others. A building area with different population totals and complex influences could be reclassified as commercial, residential, or rural. On this basis, we defined the degree of vulnerability of different land types based on an expert questionnaire, and we estimated the degree of regional ecological risk. Finally, strategies were proposed for local ecological protection, and these strategies incorporated the assessment results. In this paper, the temporal trend of nitrogen emissions in urban and agricultural systems is analyzed, and the degree of vulnerability from 2001 to 2010 is determined. The level of ecological risk in the Taiwan area of China was categorized as high, medium, or low based on comprehensive ecological risk assessment. The results indicated that the ecological risk decreased due to reduced agricultural nitrogen emissions, but increased because of higher energy consumption for transportation since 2005. In 2010, Kinmen County, Lienchiang County, Penghu County, Hsinchu City, Chiayi City, and Keelung City were classified as low-risk areas because of their low human population and agricultural intensity. However, Taichung City, Pingtung County, Tainan City, Kaohsiung City, and New Taipei City were determined to be at high risk because of higher emissions from transportation, industry, and the raising of livestock and poultry.According to the Yearbook of Environmental Protection Statistics of Chinese Taiwan, the increase in the number of motor vehicles in 2010 was an important factor in air pollution because nitrogen oxide emissions from motor vehicles accounted for approximately 45% of nitrogen emissions in air. Inspection and enforcement against pollutions sources, promotion of clean-energy vehicles and public transportation, and controlling the increase in polluting motor vehicles would be expected to decrease air pollution effectively. In addition, water quality could be improved by reducing the discharge of industrial wastewater, sewage, and livestock wastewater, and by raising the standards of wastewater discharge based on specific rainfall characteristics.However, there has still been no significant reduction in industrial waste gas, wastewater, waste residue, livestock excreta, or energy consumption. Environmental education and sustainable developmental concepts should be promoted with the aim of changing human behavior and of mitigating the negative effects of human activities.