Digital control has been widely used in dual active bridge (DAB) converters, which are pivotal parts of electric vehicles and distributed generation systems. However, the time delays introduced by the digital control could affect the performance or even lead to the instability of the digitally controlled DAB converter. In order to reduce the effect of time delay on the dynamics and stability of the system, the model predictive control (MPC) of the DAB converter is proposed based on the discrete-time iteration in this paper to compensate for the digital control delay. According to the obtained discrete-time model, the instability mechanism of the MPC DAB converters with different parameters is revealed. The simulation and theoretical analysis indicate that this method could reduce the influence of the digital control delay and increase the stable range of the system compared with the conventional control strategy. The proposed method is also revealed to have a strong compatibility and portability. In addition, the accurately predicted stability boundaries can be applied to the practical parameter design and guarantee the stable operation of the system. The experimental results are consistent with the theoretical analysis and verify the proposed method.