The vertical distribution of an emergent vegetation in wetlands and marshes is generally non-uniform due to the variations of the stem thickness and the leaf density. This study focuses on the effect of the varying vertical porosity on the hydrodynamic characteristics of the emergent vegetation flow. The new governing equation for the emergent vegetation flow with varying vertical porosity is established by applying the poroelastic media flow theory. According to the movement mechanism of the water flow in the porous media and the experimental data, the best fitted expression of the permeability is established for the emergent vegetation flow. The velocity distribution is obtained with the finite analytic method. Then, a flume experiment is performed using truncated cones to simulate the actual vegetation with varying vertical porosity. The calculated velocity distribution is compared with the measured data, which shows that the theoretical results are in good agreement with the experimental data. Finally, the influence of the vertical porosity distribution on the vegetation flow characteristics is analyzed graphically. The study can provide a useful reference and technical support for further study of the flow with a complex shape vegetation.