In low permeability porous media which permeability anisotropy is ubiquitous, the percolation of fluid no longer follows linear Darcy's Law. Oil-water two phase flow euqation of low permeability reservoir with permeability anisotropy is established based on generalized Darcy's law and starting pressure gradient, corresponding finite element program is developed and simulated based on the Finite Element Program Generator system (FEPG). The results show that energy-gathering exists in the flow event of flowing area front in low permeability reservoir. In the process of energy-gathering, the flow velocity changed little but increased rapidly as soon as the pressure gradient exceeded the starting pressure gradient of the reservoir, then gradually stabilizeed. The greater the starting pressure gradient is, the greater the near wellbore pressure drop is, the smaller the water flood swept area is. There will be more difficulties in water injection to the same extent.