Pulse-width modulation rectifier plays an important role in the field of electric energy conversion. It has many advantages such as the grid side current sinusoidal, bidirectional energy flow, and unit power factor. In order to improve the power factor, this article proposes a new control method for the three-phase pulse-width modulation rectifier, that is, direct power control strategy based on virtual flux orientation. The original concept of AC motor stator flux is introduced into the proposed scheme for the three-phase pulse-width modulation rectifier so as to remove the grid voltage sampling circuit. The instantaneous power is estimated by the virtual flux vector orientation to realize the pulse-width modulation rectifier control in unbalanced condition. The two-order filter replaces the pure integrator in this process of implementation to solve the initial value problem of this pure integrator and achieve the better filtering property. With the estimation of virtual flux, the control strategy with space vector modulation realizes the fixed switching frequency to virtual flux orientation direct power control system, where the DC side output voltage is stable, the grid side current distortion rate is low, and anti-disturbance ability is strong. Experimental results show that this method has good performance in real three-phase grid condition. The control performance meets the requirements of power quality.