A thin film micro heat-flux sensor using thermopile, which can measure the heat flow, was fabricated by a complementary-metal-oxide-semiconductor-compatible process. The combination of a ten-junction polysilicon and aluminum thermoelectric sensor with an ultralow noise preamplifier and low pass Butterworth filter has enabled the resolution of 3.4 μW power and shows the sensitivity of 2.43 mV/μW. In order to estimate the heat generation of samples from the output measurement of a micro heat-flux sensor, a methodology for modeling and simulating electro-thermal behavior in a micro heat-flux sensor with integrated electronic circuit is presented and validated. The electro-thermal model was constructed by using system dynamics, particularly the bond graph methodology. The electro-thermal system model, where the thermal domain and the electrical domain are coupled, expresses the behavior that the heat generation of samples converts thermal input to electrical output through the system model. The proposed electro-thermal system model shows good agreement with measured voltage responses.