Bayesian modeling procedure is applied to online analysis to estimate directional wave spectra based on ship motion data. The proposed method can deal with the nonstationarity of ship responses that comes from the ship maneuvers such as changes of the course and speed. In order to cope with the nonstationarity included in the time history data, instantaneous cross spectrum analysis based on T-VVAR (Time Varying Coefficient Vector Auto Regressive) modeling procedure is introduced. Moreover, Bayesian modeling procedure is transformed into an online algorithm. Some numerical experiments were carried out to examine the proposed method. Using an array of wave probes, measurements of time varying directional wave spectra were simulated. It is shown that the estimated directional wave spectra agree well with the incident wave spectrum and the proposed method can cope with the nonstationarity.