The objective of this paper is to provide a comparison between two transverse flux rotary machines (TFRM) with different topologies of stator cores. Depending on how to make stator core with laminated steel sheets, the one topology is ‘perpendicular stacking core’ and the other is ‘separated core.’ Both of the two cores have been designed considering 3-dimensional (3-D) magnetic flux path with the same output power conditions, but the core losses are quite different and it causes different magnetic and thermal characteristics. For comparison of these two topologies of stator cores, therefore, core losses have been calculated and used as a heat source in noload conditions, and the thermal stress has been also calculated. 3-D finite element method has been used for the magnetic field, thermal, and stress analysis to consider the 3-D flux path of the TFRM. After comparing the analysis results of the two topologies, experimental results are also presented and discussed.