Every year China produces huge volumes of crop straw, most of which, however, is burnt by the farmers in the fields. Burning of straw in open fields will not only reduce the contents of soil organic matter and soil moisture in the surface soil layer, but also bring about environment pollution and damage human health. To apply corn stover deep into the subsoil layer (20~40 cm), namely “Corn stover deep incorporation” (CSDI), is believed to be able to effectively solve the problem of how to utilize crop residue as resource and a number of other problems caused by burning of crop straw and further on help sequestrate carbon, raise water holding capacity, improve soil fertility and stabilize crop yield. A field experiment was conducted in a mono-cropping corn field at the Experiment Station of the Jilin Agricultural University, with four treatments, that is, CK (no-corn stover incorporated), CS (CSDI), NPK (fertilizers applied only) CS+NPK (CSDI plus fertilizers application) designed to explore effects of corn stover deeply incorporated in addition to fertilizers application on composition of soil humus and structure of humic acid (HA) in the soil. Soil samples were collected from the four treatments for analysis of humus composition with the modified humus component extraction method and for structure of HA with the IHSS method for purification and the infrared spectroscopy for element composition. Results show that treatments CS and CS+NPK were conducive to accumulation of SOC and various humus fractions in all soil layers, but did not affect PQ (percentage of humic acid in humus) much. The two treatments increased the proportion of aromatic-C in HA, and Treatment CS also increased the proportion of aliphatic chain hydrocarbon in HA, while treatment CS+NPK raised the condensation degree and lowered the oxidation degree of HA, which means the two treatments differed in mechanism of making HA stable. Besides their effects of improving the aromaticity of HA in molecular structure, Treatment CS also enhanced hydrophobicity of HA, and Treatment CS+NPK made the structure of HA more complicated.