The nonlinear Nomoto model was used as the mathematical model of ship motion, at the same time, by using the linear regression model, the random gradient algorithm with forgetting factor was analogized, and by combining with the derived random gradient algorithm, the simulation study was carried out in the case of the automobile transport ship “Hual Trooper” as example to deduce the algorithm and verify. By combining with the hyperbolic tangent function, the nonlinear innovation identification theory was obtained, and the hyperbolic tangent function was used to handle the innovation. The identification effect was compared by MATLAB programming, and the identification accuracy was obtained by calculation. Based on the model, the ship dynamics can be estimated by observing the response comparison. The design scheme has significant computational advantages, faster identification speed and higher identification efficiency.