In order to ensure deep-water flowline safety, this paper combined the axial temperature distribution model of the submarine pipeline and the distributed parameter circuit model of the skin effect electric heat tracing system; such work is conducive to proving that the heating effect of the skin effect electric heat tracing system depends on the distributed circuit parameters and power frequency of the system. Due to the complexity of the power supply device, the frequency cannot be increased indefinitely. Therefore, for the case that the input of the skin electric heat tracing system is constrained, a generalized predictive control algorithm introducing the input softening factor is proposed, and the constrained generalized predictive control strategy is applied to the electric heating temperature control system of the submarine oil pipeline. Simulation results demonstrated that the control quantity of the skin effect electric heat tracing system is effectively controlled within a constraint range, and also the values of heating power and power frequency are obtained by theoretical calculations rather than empirical estimations. Moreover, compared with the conventional control algorithm, the proposed constrained generalized predictive algorithm unfolds more significant dynamic response and better adaptive adjustment ability, which verifies the feasibility of the proposed control strategy.