Topsoil samples were collected from the typical fields under rice-oilseed rape rotation in Nanchuan, Yongchuan and Hechuan of Chongqing, and 20 soil indexes such as soil organic matter(OM), total and available contents of nitrogen (TN and AN), phosphorus (TP and AP) and potassium (TK and AK), the contents of exchangeable potassium (EK), sodium (ENa), calcium (ECa) and magnesium (EMg), and the contents of available silicon (ASi), boron (AB), iron (AFe), manganese (AMn), copper (ACu) and Zinc (AZn) were measured, factor cluster analysis was carried out by SPSS software, and then soil IFI (integrated fertility index) of all samples were calculated and divided into 5 grades for soil fertility evaluation. The results show that soils in the areas are seriously acidified, the contents of OM, TP and AP are low, and the contents of TN, AN, ECa, EMg and most trace elements are rich, but the content of AB is lack. Factor analysis shows that AB, AN, OM, AK, EK, AP, pH and ECa are the main factors affecting soil fertility. The cluster analysis shows that IFI is in the order of Nanchuan > Yongchuan > Hechuan, and soils in Nanchuan are mainly at the medium and high levels of fertility, while soils in Yongchuan and Hechuan are mainly at the low level of fertility.