Because of the ship maneuvers, such as changes of the course and the speed, ship motions in waves are regarded as a nonstationary random process, even on the assumption that the seaway can be considered as stationary stochastic process. In order to cope effectively with the nonstationarity, T-VVAR (Time Varying Coefficient Vector Auto Regressive) modeling with the instantaneous response is introduced. The procedure has the significant merit that it can be estimated by independently fitting the univariate models for each component. In order to fit the model to the data recursively, T-VVAR model is transformed into the state space model and the time varying coefficients can be evaluated by using the Kalman Filter algorithm. Using the estimated time varying coefficients, the instantaneous ship motion cross spectra can be calculated every moment. In order to examine the reliability of the proposed procedure, onboard tests were carried out.Under the stationary conditions, on the constant speed and course, the proposed method shows good agreement with the SVAR (Stationary Vector Auto Regressive) modeling analysis. Moreover, it is shown that the proposed method can estimate instantaneous ship motion cross spectra even if the speed or the course is changed. This concludes that the proposed method is a powerful tool for on-line analysis of nonstationary ship motion data. The results of these tests are shown and problems encountered on applying are reported.