In the existing iterative learning control (ILC) results for two-dimensional linear discrete systems (2-D LDS), they focus on 2-D LDS Fornasini–Marchesini model. To the best of our knowledge, the 2-D LDS Fornasini–Marchesini model is a particular case of 2-D LDS General model. This paper is first concerned with the ILC problem for 2-D LDS General model with nonidentical boundary states. A modified ILC law under three-dimensional (3-D) framework is proposed. By using 2-D LDS stability theory, perfect tracking on 2-D desired surface trajectory except the boundaries can be achieved. In addition, ILC convergence analysis for 2-D LDS General model with direct transmission from inputs to outputs is discussed. Two illustrative examples are given to show the effectiveness and feasibility of the presented ILC approach.