The study was based on the long-term black soil positioning test (beginning in 1979), and according to the input and output of soil nutrient, the soil nutrient balance of different fertilization treatments was analyzed. The dynamic characteristics of Hu molecular structure were analyzed by infrared and nuclear magnetic resonance spectroscopy, and the relationship between soil nutrient budget and the change of Hu structure was analyzed. The result shows: different fertilization measures changed the molecular structure of the inert component Hu in the soil while changing the nutrient content of black soil. From 1980 to 2014, organic and inorganic fertilizer (MNPK) treatment to meet the crop nutrient absorption, the total soil nutrient content was surplus, and the soil organic carbon content was increased and soil C/N ratio was decreased without CK treatment. At the same time, the ratio of 2 920/1 620 and 2 920/2 850, aliphatic C/, aromatic C, alkyl C/, alkoxy C and hydrophobic C/, hydrophilic C increased in the soil Hu, indicating that the molecular structure of black soil Hu became aliphatic and simplified. Fertilization can increase soil active organic carbon and reduce the content of inert organic carbon components. Organic fertilizer (M) and nitrogen, phosphorus and potassium fertilizer (NPK) could not meet the nutrient uptake of crops, and the soil nutrient deficit appeared. Infrared spectrum display, with the increase of fertilization years, the Hu of 2 920/1 620 decreased with organic manure (M) and nitrogen phosphorus potassium fertilizer (NPK) treatment, indicating that the content of aliphatic C decreased. Nuclear magnetic resonance spectroscopy showed that the treatment of alkyl C / alkoxide C decreased with NPK and non - fertilization (CK), indicating that the activity of organic carbon decreased. Although the treatments of fertilizer application without fertilization (CK) increased the soil Hu lipid C content and decreased the aromatic C content, with the increase of fertilization years, the treatment of nitrogen, phosphorus and potassium fertilizer (NPK) resulted in the change of soil Hu structure. There is a correlation between the nutrient deficit and the structural parameters of soil Hu, N, P2O5, K2O nutrient budget and total nutrient budget and 2 920/1 620 positive, aliphatic C, aromatic C was negatively correlated with the nutrient status, that can affect the structure of soil Hu. In the case of saving economic cost, the application of organic fertilizer in the rotation cycle, combined with the application of nitrogen, phosphorus and potassium fertilizer per year can meet the crop nutrient absorption, improving soil humus inert component structure while improving crop yield.