Most traditional sound field calculation methods regard the seabed as the horizontal stratified liquid sea bottom and conduct simulation analysis based on the frequency domain. Hence, the generality of the above research methods is limited to varying degrees. To accurately clarify the propagation characteristics and mechanism of very low-frequency (VLF, ≤100 Hz) sound waves in the shallow sea, a numerical calculation model is established using the finite element time-domain method (FETD) based on the three-dimensional cylindrical coordinate system. Using this model, the effects of sea-bottom topographies and geoacoustic parameters on the composition and characteristics of VLF sound fields in the shallow sea and their corresponding mechanism are investigated through the comparative analysis of various numerical simulation examples. The simulation results demonstrate that the low-frequency sound field in the full waveguide of the shallow sea is composed of normal mode waves in the seawater layer, Scholte waves at the liquid-solid interface, and elastic waves at the sea bottom. Compared with the soft sea bottom, which has a more negligible elastic impedance, the hard sea bottom is more conducive to the long-distance propagation of normal mode waves and the excitation of Scholte waves. The Scholte waves on the hard sea bottom are significantly stronger than those on the soft sea bottom. Compared with the horizontal sea bottom, the uphill topography enhances the sound energy leakage to the sea bottom. It is more favorable to receive Scholte waves at shallow depths, whereas the influence laws of downhill topography are the opposite.