An intelligent spatial reasoning method receives a plurality of object sets. A spatial mapping feature learning method uses the plurality of object sets to create at least one salient spatial mapping feature output. It performs spatial reasoning rule learning using the at least one spatial mapping feature to create at least one spatial reasoning rule output. The spatial mapping feature learning method performs a spatial mapping feature set generation step followed by a feature learning step. The spatial mapping feature set is generated by repeated application of spatial correlation between two object sets. The feature learning method consists of a feature selection step and a feature transformation step and the spatial reasoning rule learning method uses the supervised learning method.The spatial reasoning approach of this invention automatically characterizes spatial relations of multiple sets of objects by comprehensive collections of spatial mapping features. Some of the features have clearly understandable physical, structural, or geometrical meanings. Others are statistical characterizations, which may not have clear physical, structural or geometrical meanings when considered individually. A combination of these features, however, could characterize subtle physical, structural or geometrical conditions under practical situations. One key advantage of this invention is the ability to characterize subtle differences numerically using a comprehensive feature set.