Abstract: Though nitrogen is one of the necessary elements for life activities, its' excessive input in a region may cause serious environmental pollution. Hainan Island, a province in the tropics, was taken as the research object to investigate the process and characteristics of nitrogen flows in farming and animal production system. To optimize the nutrient management of this system, the relationships of nitrogen input and output changes and the temporal and spatial characteristics of nitrogen utilization efficiency were analyzed, which would provide scientific basis for the policy setting of agriculture and animal husbandry development in Hainan province. The model of NUtrient flows in Food chains, Environment and Resources use (NUFER) combining with Origin and ArcGIS software were used to analyze the temporal and spatial changes of nitrogen flows in farming and animal production system in Hainan Province from 1987 to 2016, meanwhile for the first time, the correlation of spatial and temporal variations of nitrogen flows in the farming and animal production system was analyzed under ideal and actual conditions. The results showed that the total nitrogen input increased from 134.15 Gg to 406.39 Gg, the total nitrogen output increased from 84.75 Gg to 307.77 Gg in the past 30 years. The nitrogen utilization efficiency of the farming production subsystem increased from 12.39% to 20.54%, and that of the animal production subsystem increased from 6.10% to 13%. The nitrogen utilization efficiency of the integrated system of farming and animal production increased from 12.84% in 1987 to 21.63% in 2016. In spatial distribution, the increase of total nitrogen input and output was the highest in Chengmai County and Qionghai City, respectively, while being the lowest in Wuzhishan City. In the animal production subsystem, the increase of total nitrogen input and output was the highest in Wenchang City and Danzhou City, respectively, while being the lowest in Wuzhishan City. The results show that the nitrogen input of farming and animal production system in Hainan Island increased continuously from 1987 to 2016, with the low nitrogen utilization efficiency, the big spatial difference, and the high soil nitrogen surplus. The correlation analysis showed that the farming production subsystem and the animal production subsystem were disjointed seriously. Therefore, in order to improve the efficiency of nitrogen flows and promote the sustainable development in Hainan Province, it is necessary to increase the yield of local feedstuff, make rational use of fertilizer, recycle livestock and poultry manure, further optimize the layout of agriculture and animal husbandry development, and establish a highly efficient production system for farming and animal husbandry.