This paper aimed to study and analyse the distribution of PAEs in cotton stalk and biological accumulation process. Cotton stalk (not including cotton peach shell) was divided into three section (Upper, middle and lower), and smashed by the grinder. Each section’s PAEs was extracted by ultrasonic method, and Ultrasonic’s extraction was detected respectively by gas chromatography method. The results indicated that each sample Contained PAEs, PAEs had transferred from environment to soil, then to plants. Six kinds of PAEs (DMP, DEP, DIBP, DBP, DAP, DEHP) using GC analysis had a good linear relationship in a certain range, and a high degree of six kinds of material separation. The different section of cotton stalk had different content PAEs. Cotton stalk of the amount of PAEs arrive 158.86 mg/kg, DEHP in cotton stalk reached 125.300 mg/kg. It was the highest in six kinds of PAEs, cotton stalk of PAEs was rich in the middle section.