The problem of the productivity prediction of the low permeability wells is considered. By analyzing the seepage flow mechanics mechanism of low permeability wells, and considering the factors of threshold pressure gradient(TPG), stress sensitivity and fracturing stimulation, the production model of low permeability wells is established. The grey model of well productivity prediction(WPGM(1,1)) is obtained by using the grey theory, also the formula of parameters solution and the algorithm of solution of the model are derived. The accuracy of WPGM(1,1) model is improved by function transformation, and the output of low permeability wells is predicted by using the WPGM(1,1) model. Numerical example analysis show that the proposed algorithm and model are feasible and effective.