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Compared with normal reservoirs the reservoir with very low permeability had the characteristics of non-Darcy flow and stress sensitivity. Through the analysis of the mathematical model of the numerical simulation for this kind of reservoir the special input and output files, parameters and variables, storage of the matrix of the linear equations and method of calculation should be specially designed. In the programming based on the characteristic the parameters in input files and output files should be optional, the variables should be notional and be deleted timely, matrix of the linear equations should be stored by two 1D array instead of 2D array to save the space, and optimization of speed should focused on the formation of matrix and the equation solving. Numerical simulation software developed using Fortran in Linux could run more rapidly and more stably than other editions.