The main advantage of polychromatic sets-based assembly tolerance representation model is that the number of feature types to be processed is larger. However, the number of recommended assembly tolerance types generated by the model is somewhat large for the same feature surfaces. Furthermore, the model cannot be directly applied to further assembly tolerance analysis and synthesis due to the fact that the information of degrees of freedom cannot be processed in polychromatic sets. To further reduce the number of recommended assembly tolerance types and to lay foundation for further assembly tolerance analysis and synthesis, a spatial relation layer is introduced into the polychromatic sets-based model and an assembly tolerance representation model based on spatial relations for generating assembly tolerance types is proposed. The proposed model is hierarchically organized and consists of part layer, assembly feature surface layer, spatial relation layer and assembly tolerance type layer. Each layer is defined with an adjacency matrix, respectively. By the mapping from spatial relations to assembly tolerance types, the number of recommended assembly tolerance types generated by the mapping from feature surfaces to assembly tolerance types is able to be further reduced. In addition, the information of degrees of freedom can be attached in the elements of adjacency matrices when recommended assembly tolerance types are generated by spatial relations so that the proposed model can be directly applied to further assembly tolerance analysis and synthesis. The effectiveness of the proposed model is demonstrated by an approach for generating assembly tolerance types and a practical example.