To further explore the influential factors of soil available microelements, the farmland soils in in Jiangjin of Chongqing were taken as the study objects, the data of 1 265 sampling sites, together with cropping systems and parent rock types, were used to construct the regression model of soil microelements and random forest model (RF) was used to quantitatively analyze the relative importance of influential factors of soil available microelements. The results showed that the prediction model with the cropping system and the parent rock type was higher than the conventional regression model, the fitting degrees (R²) of available Fe, Mn, Cu and Zn were increased by 9.20%, 38.99%, 20.75% and 29.96%, respectively, compared with the conventional regression model. The prediction accuracy was improved for soil available Fe, but not for available Mn, Cu and Zn. Soil nutrients and cropping system were relatively important for the contents of available microelements in farmlands, and among of them, the effects of pepper and rice planting as well as soils derived from Suining Formation were relatively important. This study could provide theoretical and scientific bases for reasonable fertilization and management of Jiangjin farmlands.