Amongst the various topologies of multi-input multi-output (MIMO) DC-DC converters, single-inductor MIMO (SI-MIMO) converters have the advantages of a reduced component count, a simpler structure, and low cost. These converters are suitable in electric vehicle (EV) applications involving variable ports, essential for performing different functions. Digital control in SI-MIMO converters is promising for enhancing transient performance due to its numerous benefits. However, delays in digital control, particularly computational and pulse width modulation (PWM) delays, can negatively impact the performance of DC-DC converters. Multi-sampling and double PWM update methods can mitigate these control delays, but they often necessitate complex control schemes, adding computational burden. In this work, an advanced multi-sampling PWM technique, integrating sample shift and multi-sampling, is proposed while employing a simple digital PID control scheme. The proposed method was tested for a shared-switch SI-MIMO converter with battery discharging and charging modes in the MATLAB/Simulink environment and compared with the conventional single- and multi-sampling PWM methods. The results demonstrated that the proposed method significantly improved the converter performance, surpassing the conventional single- and multi-sampling PWM methods. In the battery discharging mode, utilizing the proposed method, the output voltage achieved a settling time of 0.075 s in response to a step change in its reference, significantly outperforming multi-sampling, which yielded a settling time of 0.124 s, and single sampling, which exhibited an even longer settling time of 0.898 s. It also demonstrated a minimal overshoot of 0.06 volts compared to 1.5 volts with multi-sampling during the step change in the input voltage. Similarly, in the battery charging mode, upon a step change in the reference output voltage, the proposed method effectively minimized the overshoot of the output voltage to 0.845 volts compared to 1.175 volts with multi-sampling, and it decreased the inductor current settling time to 0.296 s from 0.330 s recorded under multi-sampling. These findings underscore the potential of the proposed method in enhancing the digital control performance of SI-MIMO DC-DC converters in electric vehicles.