Axial Flux Permanent Magnet Synchronous Motor (AFPMSM) attracts increased attention in recent years due to the inherent high torque density. The yokeless and segment armature is one of the most advanced structures, with reduced axial length and increased efficiency. For the segment armature fixed axial flux motors, encapsulating material is required between the winding and the structure fins. However, it is difficult to calculate the contact thermal conductivity between the fins and windings for the machine thermal performance prediction, due to the multiple material components and different interface pressure. For the complicated materials characteristics analysis, Grey Box theory is proposed to predict the thermal behavior of the non-metallic mixture in the contact region in this paper. Firstly, the axial flux motor topology is presented, as well as a single sector model. Then the Grey Box frame is introduced with the testing rig to train the critical parameters that will be used in thermal model. Through genetic algorism, the thermal conductivity and heat capacity of mixture materials in the area of the segmented armature contact surface are obtained. Finally, the equivalent thermal conductivity in the contact region is updated to a 3D thermal model, which are experimentally validated on a sector model and a prototype motor.