The soil aggregate stability is a key property of soil quality and reflects soil quality and anti-erosion ability. The transition matrix between initial and final aggregates condition was established by modifying Niewczas and Witkowska-Walczak's method by not considering the artificial weights and each size of aggregates fraction on the basis of three reasonable assumptions, and soil aggregate stability index (ASI) was formed through preserving each size of aggregates probability. This ASI is identical to the result by reference, and the transition matrix can be showed to evaluate the soil aggregates stability. Using the transition matrix was furthermore to analyze anti-breaking ability of different size aggregate by reference material. We found there were different effects for each size aggregate by four methods, simulation rainfall, one cycle of wetting–drying, ten cycles of wetting–drying, and Yoder wetting–sieving. The Yoder wetting–sieving is a severe method that destructed soil aggregates. The ASI by modifying transition matrix method was used to evaluate the aggregates stability under different land utilization in Karst region in Chongqing, China. The ASI of agricultural utilization was lower than abounded cultivated land, shrub-grass land, secondary forest land, and primeval forest land. For some selected soil properties, when SOM content was <60 g/kg, ASI increased along with the SOM increase. Once the SOM content was >60 g/kg, the ASI was almost unchanged. The sorption moisture content of air-drying acutely affected ASI too, and the ASI increased along the sorption moisture increasing. SOM content and sorption markedly affected the preserving probability of larger aggregates such as 10–5, 5–3, 3–2, 2–1, and 1–0.5 mm size class. Although CaCO3 and clay content did not influence preserving probability of each size class of aggregates fiercely, but the influence on small aggregates was higher than that of larger aggregates. The modified transition matrix method could not only calculate soil aggregates stability index, but also analyze more parameters of aggregate experiment, and bring out the each size aggregates characteristics. Thus, the modified transition matrix method could be a better tool to understand soil quality.