Abstract: Pot experiment in greenhouse with different application rates of bioorganic fertilizer on three kind soils with low, middle, high organic matter (SHM, SMM, SLM) was carried out three years. Effects of fertilization on soil organic matter fractions, cotton nutrient absorption and yield were studied. The results showed that the soil organic matter and labile organic matter fractions, cotton nutrient absorption and yields were increased by the application fertilizer three years later. The contents of soil organic matter and labile organic matter fractions (organic matter, labile organic matter, middle labile organic matter and high labile organic matter) were also increased with the increase of the application rates. The increase ratio of labile organic matter was higher than that of the organic matter after the three years. It indicated that the application of bioorganic fertilizer could improve the quality of soil organic matter. The biggest amount of cotton nutrient absorption were treatments with application 20-30 g/kg bioorganic fertilize to higher, middle organic matter contents soils, but at 40 g/kg to low organic matter contents soil. According to cotton yields, application 20, 20 and 40 g/kg of bioorganic fertilize to higher, middle, and low content of organic matter soil, and the yields were increased by 54.05%, 37.15% and 104.08% compared to control treatment(no fertilizer application), respectively. The correlation analysis showed that the correlations were better between soil organic matter fractions, cotton nutrient absorption quantity and yield with the soil organic matter content from high to low. There were significantly correlation between cotton nutrient absorption quantity and yield in the three soils.