In this paper, the iterative learning control (ILC) technique is extended to multi-input multi-output (MIMO) systems governed by parabolic partial difference equations with time delay. Two types of ILC algorithm are presented for the system with state delay and input delay, respectively. The sufficient conditions for tracking error convergence are established under suitable assumptions. Detailed convergence analysis is given based on discrete Gronwall’s inequality and discrete Green’s formula for the systems with time-varying uncertainty coefficients. Numerical results show the effectiveness of the proposed ILC algorithms.