The aim of this study is to explore the spatial variability of soil moisture characteristic curve with the long term fertilization, and find out the influencing factors of that variability. Based on the long term experiment in Agricultural Ecological Experimental Station of the Loess Plateau of Chinese Academy in Changwu, the soil moisture of different suction with the long term fertilization was measured using the method of high-speed centrifuge, and the water characteristic curves were obtained by the mathematical models of Van Gennuchten. Then, the parameters such as soil moisture characteristic curves, water capacity, water supply and soil moisture availability with the multiple fertilizations were compared. The results showed that the significant variations of soil moisture characteristic curve were attributed to the changes of soil structure caused by the long-term fertilization. Chemical fertilizers (N, NP) destroyed soil structure, which reduced the soil water capacity. Organic fertilizer (M, NPM) increased the soil organic matter content, and then improved the soil structure, which increased soil water capacity. The effectiveness of the soil moisture of applying manure (M, NPM) was significantly higher than that of N, NP, CK. The water supply capacity and soil water availability were ranked as N, CK, NP, NPM, M.