This paper validates a system identification method using mathematical optimization using sea trial measurement data as a benchmark. A fast time simulation tool, SIMOPT, and a Rheinmetall Defence mathematical model have been adopted to conduct initial hydrodynamic coefficient estimation and simulate ship modelling. Calibration for the environmental effect of sea trial measurement and sensitivity analysis have been carried out to enable a simple and efficient optimization process. The optimization process consists of three steps, and each step controls different coefficients according to the corresponding manoeuvre. Optimization result of Step 1, an optimization for coefficient on x-axis, was similar compared to values applying an empirical regression formulae by Clarke and Norrbin, which is used for SIMOPT. Results of Steps 2 and 3, which are for linear coefficients and nonlinear coefficients, respectively, was differ from the calculation results of the method by Clarke and Norrbin. A comparison for ship trajectory of simulation results from the benchmark and optimization results indicated that the suggested stepwise optimization method enables a coefficient tuning in a mathematical way.