Applications, theoretical analysis and numerical methods are introduced for the simulation of mechanical models and principles of the porous flow in high temperature, high salt, complicated geology and large-scale reservoirs in this paper. Considering petroleum geology, geochemistry, computational permeation fluid mechanics and computer technology, we state the models of permeation fluid mechanics and put forward a sequence of implicit upwind difference iteration schemes based on refined fractional steps of the upstream, which can compute the pressures, the saturation and the concentrations of different chemistry components. A type of software applicable in major industries has been completed and carried out in numerical analysis and simulations of oil extraction in Shengli Oil-field, which brings huge economic benefits and social benefits. This software gives many characters: spatial steps are taken as ten meters, the number of nodes is up to hundreds of thousands and simulation time period can be tens of years and the high-order accuracy can be promised in numerical data. Precise analysis is present for simplified models of this type and that provides a tool to solve the international famous problem.