The throat topography (or called “gate”) is a typical high energy consumption zone at Pearl River Estuary. Research on the turbulent kinetic energy dissipation induced by the throat topography is important to the explanation of the Pearl River Estuary dynamic phenomenon and understanding of dynamic estuarine processes. A physical model was designed for study of turbulent energy dissipation induced by throat topography. The high frequency velocity was collected by SonTek 16MHz ADV. Turbulent energy dissipation was calculated by inertial dissipation method for channel flow and jet flow induced by the throat topography. Turbulent energy dissipation induced by the throat topography is 100～1000 times than that in common channel. From the local turbulent equilibrium and energy transfer theory, the higher spatial gradients of velocity ,turbulent stress and more smaller scale eddies produced by the throat topography is the important reasons that make the turbulent energy dissipation rate increase 2~3 order of magnitude.