Proper use of phase-controlled switching technology by controlling the making or breaking of the circuit breaker (CB) at predetermined phase angles of current or voltage can improve the service life of the CB, avoid relay protection device from mal-operation, and reduce the impact on the power grid when power equipment or load is energized or taken out. This paper proposes a novel phase-controlled switching method to address the influence of residual flux for three-phase wye winding unloaded transformers with three limbs, such as large capacitor variable frequency transformer or mine explosion-proof transformer. The optimal operation phase angle for CBs is firstly obtained via theoretical analysis. A model based on the alternative transients program/the electromagnetic transients program (ATP/EMTP) is then built to simulate the transient procedure of a power transformer during breaking and making. The simulated results confirm that the proposed switching strategy can reduce the excitation inrush current effectively when the unloaded transformers are energized. The experimental results reported in this paper are used to validate the accuracy and effectiveness of the phase-controlled switching strategy.