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In this paper, iterative learning control problem of continuous-time system with variable initial condition is considered. Based on the two-dimensionality of the overall learning system, a continuous-discrete two-dimensional (2D) learning system is established. The proposed error system describes entire dynamics involved in iterative learning including the dynamics between tracking error and variable initial state. According to the 2D system theory, a learning error estimate is given and the design method for learning matrices is also proposed. The simulation results demonstrate the performance of our proposed method.