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Heat flux measurement method with thin film resistance sensor in a premixed gas combustion field has been studied to develop an accurate heat flux sensor, and to grasp and improve a heat transfer loss of the engine in SIP (Cross-ministerial Strategic Innovation Promotion Program) innovative combustion technology project. The MEMS technology was introduced to satisfy the requirement of the accurate heat flux measurement with high temporal, spatial and heat flux resolution for a turbulent heat transfer in the engine. The thin film resistance sensors of 250 to 1000 micron scale were fabricated on the Si substrate, and then a calibration method, measurement characteristics and response to the combustion were studied. Since the heat flux was measured through the surface temperature measurement and the transient heat conduction analysis of the sensor, accurate data and an exact thermal model are required. The heat flux calibration using self-heating showed a good agreement between the excited heat flux of 400 kW/m2 level and measured one with an error less than 10 kW/m2 for the wide frequency range from 200 Hz to 8 kHz by introducing an interfacial thermal resistance in the thermal model. The developed measurement system showed heat flux peak of 250 kW/m2 level with noise of 10 kW/m2 level against a butane-air premixed gas combustion in an open chamber. Heat transfer analysis showed that the heat flux trend after the peak can be explained by heat conduction between the burnt gas and the sensor wall. It was also demonstrated that the developed system can measure heat flux down to 10 kW/m2 and up to 5 kHz frequency range. Good prospect of the heat flux sensor for the engine application was obtained with the sufficient accuracy and the resolutions.