The input estimation method (IEM) is proposed in this research to estimate the real-time time-variant core heat flux of electronic components. The IEM is an on-line real-time estimation method, which combines the Kalman filter mechanism and recursive least-square estimation (RLSE). On the premise that there exists both system processing error and measurement error, using temperature measurements measured from the exterior of the device package, the core time-variant heat flux of the device can be precisely estimated inversely.