A combined time-frequency domain method is proposed to analyze the stresses of barge-jacket assembly during transportation. Starting with the motion of analysis in frequency domain, the time history of waves and motions in random seas are simulated, then the stresses are determined in time domain. The stress autocorrelation functions are calculated and the stress spectra and statistical characteristics are obtained through Fourier transformation. A computer program has been developed. The effects of barge flexibility and the forces caused by the immersion of jacket have been discussed.