The Okinawa Trough is an ideal area for conducting the dynamics research of marginal sea basin. On the basis of sequence division to several seismic sections in the Southern Okinawa Trough(SOT), the paper investigated its tectonic subsidence characteristics by coupling analysis of back stripping and forward simulation. Quantitative analysis of the tectonic subsidence using back stripping technology indicates that the Southern Okinawa Trough presents a late but high development degree, with 60 percent of total subsidence amount occurring within 0.1 Ma. The northern part of SOT displays a continue subsidence process, while the southern part of SOT presents an differential subsidence process (uplift relatively) due to the ‘Taiwan arc continent collision’. The comparison analysis between observed tectonic subsidence using back stripping technology and theoretical tectonic subsidence predicted by forward simulation shows that in SOT the initial subsidence was in progress and there were anomalous subsidence in both southern and northern ends. The early anomalous subsidence in the southern end was an result of ‘Taiwan arc continent collision’, while the late subsidence and anomalous subsidence in the northern end can be interpreted as the effect of dynamic subsidence. Comparison of tectonic subsidence amount and appearance of dynamic subsidence indicates the trough experienced a tectonic process evolving from north to south.