To tackle the problems, such as declining soil organic matter content and degrading farmland quality in the black soil region of Jilin Province, soil samples were collected from a 20-year long-term stationary field experiment on fertilization at the Gongzhuling National Black Soil Fertility and Fertilization Efficiency Monitoring Base for analysis of composition and morphological structure of soil humus by means of modern analytical methods, like NMR Spectroscopy and IR Spectroscopy and exploration of their dynamic variation as affected by fertilization method. It was found that fertilization methods had some significant effects on characteristics of soil humus in cultivated layers. In the field experiment, the component of aliphatic structure in soil humic acid (HA) increased significantly in Treatment S+NPK (conventional NPK plus incorporation of corn stalks) and Treatment M NPK R (conventional NPK plus organic manure and crop rotation; the content of oxhydryl in soil HA increased obviously in Treatment M NPK (conventional NPK plus organic manure) the content of free carboxyl increased too in Treatment S NPK; the component of methyl, methylene and methenyl structures in fulvic acid (FA) increased obviously and free carboxyl did too in Treatments S NPK, M NPK and M NPK R; and inorganic carbonate and silicate increased in the FAs exacted from the soil of Treatment NPK, which means long-term application of chemical fertilizer may cause reduction of free FAs and exhaustive utilization of soil may lead to increase in FA of iron- and copper-bounded or complexed form. Obviously, fertilization methods vary in effect on elemental composition of HA and FA in black soil, and nevertheless all of them reduce HA C content and increase HA N content and FA C, FA N and FA H contents and reduce FA O content. Treatments F (fallow) and M NPK R increased soil HA N content the most significantly, while Treatments F and S NPK reduced soil HA C content the most significantly. Compared with CK, Treatment F reduced soil HA H content markedly, while all the other treatments increased the content markedly. F fertilization, regardless of method, reduced of oxidation degree of soil FAs. Obviously Treatments F, M NPK R, M NPK were better than treatment NPK in adjusting C, H, O and N components in soil FAs. It is, therefore, concluded that elemental composition of soil humus can be regulated by using different fertilization methods.