Three-phase pulse width modulation (PWM) rectifiers are essential power conversion devices in AC microgrids. However, DC load disturbances in the microgrid are unknown and filter capacitor parameters are imprecise, which will directly affect the control performance of the rectifiers. Therefore, a discrete model reference adaptive control (MRAC) method for three-phase PWM rectifiers is proposed to realize the high-performance operation of three-phase PWM rectifiers under the coexistence of DC load disturbances and unknown filter capacitance parameters. Firstly, a discrete model of the three-phase PWM rectifier is established. Secondly, based on the model reference adaptive control theory, a voltage-loop discrete adaptive controller and an adaptive law for load and filter capacitance parameters are designed respectively. The adaptive law is used to adjust the load and filter capacitance parameters in the adaptive controller in real time, which not only effectively improves the tracking accuracy of the output voltage of the three-phase PWM rectifier, but also significantly enhances its robustness against load disturbances and parameter variations of the filter capacitor. Meanwhile, the stability and convergence of the proposed controller are verified by combining the discrete Lyapunov stability theory. Finally, simulation and experimental results show that the designed adaptive law can accurately estimate the load and filter capacitance parameters. Compared with the double-loop proportion integral (PI) control method, the proposed control method exhibits shorter load regulation time, smaller voltage sags and lower grid-side current total harmonic distortion (THD), along with strong adaptability to load disturbances and high robustness against filter capacitance parameter uncertainties.