Motivated by the cooling process control of industrial jacketed crystallizers, this paper proposes a discrete-time domain model identification method and a model-based control scheme for such a cooling process based on a computer-aided control device. By using an input excitation of a rectangular wave to comply with practical constraints of a cooling circulator for implementation, a bootstrapping identification method is developed to establish a discrete-time integrating-type model with integer delay for describing the temperature response of the cooling process. Consistent parameter estimation against measurement noise is addressed with a proof. Correspondingly, a discrete-time two-degree-of-freedom control design is developed for the convenience of implementation in a sampled control system, which can improve the set point tracking without overshoot and load disturbance rejection. Illustrative examples from the literature and an application to a 4-L crystallizer are given to show the effectiveness and merit of the proposed model identification algorithm and control method.