Drilling results suggest that the thickness of natural gas hydrates (NGHs) in the Shenhu area, South China Sea (SCS) are spatially heterogenous, making it difficult to accurately assess the NGH resources in this area. In the case that free gas exists beneath hydrate deposits, the frequency of the hydrate deposits will be noticeably attenuated, with the attenuation degree mainly affected by pore development and free gas content. Therefore, the frequency can be used as an important attribute to identify hydrate reservoirs. Based on the time-frequency characteristics of deposit deposits, this study predicted the spatial distribution of hydrates in this area using the frequency division inversion method as follows. Firstly, the support vector machine (SVM) method was employed to study the amplitude versus frequency (AVF) response based on seismic and well logging data. Afterward, the AVF response was introduced as independent information to establish the nonlinear relationship between logging data and seismic waveform. Then, the full frequency band information of the seismic data was fully utilized to obtain the results of frequency division inversion. The inversion results can effectively broaden the frequency band, reflect the NGH distribution, and reveal the NGH reservoirs of two types, namely the fluid migration pathway type and the <i>in situ</i> self-generation self-storage diffusion type. Moreover, the inversion results well coincide with the drilling results. Therefore, it is feasible to use the frequency division inversion to predict the spatial distribution of heterogeneous NGH reservoirs, which facilitates the optimization of favorable drilling targets and is crucial to the resource potential assessment of NHGs.