A new methodology is proposed to design digital PID controllers for multivariable systems with time delays. Except for a few parameters that are preliminarily selected, most of the PID parameters are systematically tuned using the developed plant state-feedback and controller state-feedforward LQR approach, such that satisfactory performance with guaranteed closed-loop stability is achieved. In order to deal with the modeling error owing to the delay time rational approximation, an IMC structure is utilized, such that robust stability is achieved, without need for an observer, and with improved online tuning convenience. Using the prediction-based digital redesign method, the digital implementation is obtained based on the above-proposed analog controller, such that the resulting mixed-signal system performance will closely match that of the analog controlled system. An illustrative example is given for comparison with alternative techniques.