The residual flux (RF) in three-phase transformers can dramatically increase the inrush current when the transformer is energized. The RF can also severely interfere with diagnostic tests, such as the frequency-response analysis (FRA) test. However, there is no effective method to fully eliminate the RF in the core of a three-phase transformer. Additionally, there are few relevant experimental reports on methods to accurately measure the RF in the magnetic core of a three-phase transformer; this measurement is important for evaluating the demagnetization results and phase-controlled switching strategies. Hence, this paper proposes an improved flux-controlled variable frequency-constant voltage (VFCV) strategy combined with core flux equalization to simultaneously eliminate and measure the RF of a three-phase transformer core by applying a low-power electronic device. The effectiveness and accuracy of the proposed strategy are validated by the simulation and experimental tests of a 10 kV distribution transformer and a 500 kV delta-connection three-phase separating transformer. The results reveal that the RF can be eliminated to less than 1% of the knee point flux and that the measurement is fairly accurate.