In order to investigate the influence of the vertical variation of porosity on open-channel flow with submerged vegetation, vertical non-homogeneous stumps and stems in submerged vegetation flow are simulated with truncated cones in a laboratory flume. First, porosity is defined as a function of water depth. A new governing equation for vegetation flow is established on the basis of the poroelastic media flow theory, and its analytical solution is obtained with the finite analytic method. Then, the fitting expression of permeability is established with experimental data, which shows the variation in permeability with vertical porosity and vegetation density. Finally, the calculated velocity distribution is compared with the measured velocity distribution. The theoretical results are in good agreement with the experimental data, which indicates that the theoretical formula accurately and practically predicts vertical velocity distribution in complex open-channel flow with submerged vegetation.