Application of synthetic nitrogen (N) fertilizer has been playing a critical role in enhancing the supply of food to an increasingly growing world population. However, large inputs of mineral N fertilizer in excess of the crop requirements may lead to low N use efficiency and cause a series of negative environmental impacts, such as eutrophication of surface waters, nitrate pollution of groundwater, soil acidification and greenhouse gas emissions. Such environmental problems are getting worse due to predictable increase in the use of mineral N fertilizer in the future. Therefore, optimal N fertilizer management strategies synchronizing N supply with crop demand should be developed to maintain crop yield and economic profit while minimizing negative environmental impact. Organic fertilizer as substitute for mineral N fertilizer has been advocated and practiced to increase soil carbon (C) sequestration and improve soil fertility. It has also been suggested that application of organic fertilizers, either alone or in combination with mineral N fertilizers, is effective in mitigating N-related pollution, improving soil fertility, and increasing crop yield. At present, how to fertilize rationally, improve crop yields, build up soil fertility and meanwhile maintain a sound ecological environment is one of the major challenges to agricultural research. Which step of N transformation in the soil would long-term application of organic manure affect thus influencing N supplying capacity and N retaining mechanism of the soil? What is the mechanism behind long-term application of organic manure decreasing N-related pollution and the increasing crop yield? This review elaborated effects of long-term fertilization on key processes of soil nitrogen cycling in agricultural soil in expectation to provide some theoretical basis for rationalization of long-term fertilization and improvement of N fertilizer utilization rate. The review proceeded from the angle of primary N transformation rate of the processes of soil nitrogen cycling to discuss effects of fertilization (mineral or organic fertilizers) on key processes of the soil nitrogen cycling. Soil N mineralization and assimilation are two crucial links in the cycling and factors that determine soil N supplying capacity. Long term application of nitrogen fertilizers could increase soil organic N and C contents and provide crops with available N slowly through mineralization of soil organic N and subsequent nitrification. Large volumes of long-term fertilization experiments demonstrate that long-term application of N fertilizers could stimulate soil primary N mineralization rate by increasing soil organic N and C contents. Long-term application of chemical N fertilizers or organic manure both have some influence on assimilation of soil ammonium nitrogen, which is reflected as a whole in better effect of organic manure raising soil ammonium assimilation rate than that of chemical fertilizer. Generally speaking, long-term application of N fertilizer, especially organic manure, could significantly increase soil N primary mineralization and assimilation turnover rate, and stimulate soil autotrophic nitrification, too, which may be attributed to the difference between chemical fertilizer and organic manure in stimulation mechanism. The experiments also demonstrate that the application of either chemical fertilizer or organic manure could increase soil denitrification rate, and the effect is more apparent with the application of organic manure. Being a substitute of chemical fertilizer, organic manure has been advocated and used to improve soil fertility and carbon sequestration capacity. Researches indicate that the application of organic manure, either singly or in combination with chemical fertilizers can effectively reduce nitrate pollution, and improve soil fertility and crop yield, but in terms of application rate, it could not be said as the more the better. Like chemical fertilizer, organic manure, if applied excessively, may also increase the risk of N loss. Rational fertilization with its impact on eco-environment taken into consideration is the only way to raise crop yield, maintain soil fertility and pursue sustainable development of the agriculture. The study on effects of long-term fertilizer on various processes of soil N cycling will help us understand how long-term fertilization affect soil N supplying and retaining capacities and lay down a scientific basis for rationalizing N fertilization.