Low-temperature oxidation is an important stage before spontaneous combustion of cotton. It is of great significance to explore the changes of cotton microstructure during low-temperature oxidation to prevent cotton fire. The typical long-staple cotton and unginned cotton were selected for pre-oxidation treatment. The oxidation characteristics and apparent activation energy of cottons at different oxidation temperatures were studied by TG and DSC measurement. The micro characteristics of cottons were studied by SEM, X-ray diffraction and FTIR. The results showed that low-temperature oxidation stage of cotton could be divided into initial pre-heating stage (60 °C ∼ 90 °C) and rapid oxidation stage (120 °C ∼ 210 °C). The cotton was mainly in the physical adsorption stage below 90 °C, the apparent activation energy of cotton was positive, and the content of various functional groups did not change significantly. At 90 °C ∼ 210 °C, the cotton was mainly at the stage of chemical adsorption, the apparent activation energy was negative, and the content of various functional groups changed significantly. 120 °C could be regarded as the active temperature point, which the average diameter and crystallinity of long-staple cotton and unginned cotton were the largest. At 120 °C, cellulose macromolecules began to depolymerize. The glucose ring of cellulose broke to form l-glucose, which was then broken down into CO2 and water. Further, the reaction process of cotton at low-temperature oxidation stage was proposed.