This paper studied the changes of soil aggregate stability and organic carbon in different tobacco cropping years and their influential factors in Liangshan and Panzhihua of Sichuan Province through field sampling and laboratory analysis. The results showed that water-stable aggregates were significantly damaged during in period of 0-5 years of tobacco cropping, the MWD of soil aggregates in red soil, purple soil and paddy soil decreased by 68%, 64% and 52%, respectively. Meanwhile, the destruction of the water unstable aggregates was concentrated in the period of 3-5 years of tobacco cropping, and the MWD of the soil aggregates in red soil, purple soil and paddy soil reduced by 31%, 9% and 17%, respectively. The content of organic carbon affected on the water stability of soil aggregates, especially in paddy soil and purple soil. Organic carbon was mainly distributed in aggregates with sizes of >5mm and < 0.25mm. With the increase of tobacco cropping year, the contents of organic carbon were significantly decreased in purple soil and paddy soil, especially in aggregates with sizes of >5mm and < 0.25mm, and organic carbon was distributed more uniformly in different size aggregates. It proves that continuous tobacco cropping is harmful to soil aggregation and accumulation of organic carbon, and organic fertilizer should be applied to protect and improve soil aggregation in purple soil and paddy soil.