Rotor winding inter-turn short circuit a common fault in hydro-generators. This fault would change the temperature, stress, and other thermal fields of a rotor and threaten the safe operation of the generator. In this paper, the Three Gorges hydro-generator is taken as an example. Mathematical models of three-dimensional temperature field and thermal stress field of rotor magnetic poles are established based on heat transfer theory and solved by finite element method. The temperature field, thermal deformation, and thermal stress distribution of magnetic poles in rotor winding inter-turn short circuit are calculated. On the basis of the calculation, the effects of the different turn numbers and positions of short circuit on the temperature, thermal deformation, and thermal stress of rotor magnetic poles are further studied. It is concluded that the thermal stress of the winding adjacent to the shorted turn would decrease, the thermal stress of the winding farther away from the shorted winding would increase, and so on. The results of this paper can provide references for inter-turn short circuit fault diagnosis and lay a foundation for the further studies of related faults.