The flow past a submerged vertical cylinder with porous structure in open channels was investigated numerically using OpenFOAM. The numerical simulations were conducted to compare the horseshoe vortex and the vortex shedding for cases of cylinders with and without porous bottom. The flow fields were calculated by solving the Three-Dimensional (3-D) Reynolds-Averaged Navier-Stokes (RANS) equations with the SST k-omega turbulence model for incompressible viscous flow by PISO algorithm. The flow mechanism was investigated by the results of velocity fields and velocity contour. The form of porous structure influenced the flow structure near the bed. The horseshoe vortex and the vortex shedding were weakened as the height of the porous section became higher, while the domain of influence of the vortex behind the cylinder was getting narrower, which may lead to a weaker scouring near the cylinder than that without porous bottom.