In order to precisely control the flying height of TFC head with consideration of microscale thermal effect, the thermal conducting characteristics and the influencing factors on TFC slider which is in an operation and multi-physics field condition were analyzed. In consideration of rarefaction effect of ultra-thin film at the head/disk interface, the models of slider heat conduction, air bearing surface heat transfer, and gas flow were established; the thermal deformation mechanism and the effect of thermal conduction on dynamic characteristics of slider were analyzed by using finite element method. Results show that the thermal conducting model and the proposed modification of Reynolds equation in this study are suitable for solving the problems of thermal deformation and dynamic characteristics of head slider. The main parameters that influence the thermal property of slider can be considered to be the heater height, heat generation rate, and the heat conductivity coefficient of the material. The change of the slider flying height is determined by the air bearing force and the air bearing surface thermal extrusion at the head/disk interface. Simulation results provide a basis for the design of heater in head slider and analysis of dynamic characteristics of air bearing.