Abstract: Drilling results suggest that natural gas hydrates in the Shenhu area of the northern continental slope of South China Sea are obviously heterogenous in both vertical and horizontal directions, which brings about great difficulties to evaluate accurately the amount of hydrate resources. Based on integrated well-seismic data analysis for gas hydrates distribution characteristic, using frequency-divided inversion of SVM method in this research to predicted the hydrate spatial distribution in the area. Frequency –division inversion which is using logging and seismic data, application the method of support vector machine (SVM) under different frequency versus amplitude response (AVF), introduced the AVF as independent information, establish the nonlinear relationship between well logging and seismic waveform, make full use of the whole frequency band in the seismic, thus high resolution inversion results are obtained. The inversion results are in good agreement with the facts disclosed by drilling wells in this paper. Therefore, the method is believed feasible to the prediction of thickness heterogeneity. The research results also revealed that the mainily factors which control the thickness heterogeneity of gas hydrates include not only temperature-pressure conditions. Tectonic movement was frequent since late Miocene in the study area and deep pyrolysis gas shall be transported up along the vertical channels such as gas chimneys and faults, which is to form thick layer of “leakage type gas hydrate deposits fluid transported”, at the same time, the biogas generated by microorganisms will be accumulated in the thin layers of seabed sediments to form the “autochthonously generated and self-stored diffusion type” gas hydrates reservoir.