A numerical study of transient conjugate heat transfer on micro heater in a micro-channel substrate under pulsed heating was conducted. It was found that the time constant is not affected by the pulse heating magnitude at same operating condition. Furthermore, the time constant increases with low substrate thermal diffusivity, low Reynolds number, and large channel diameter. Since the time constant is a dominant parameter to characterize transient heat transfer, it should be considered for transient convective heat transfer coefficient.