Abstract: A 5-layer primitive equation prediction model is developed in a modified σ-coordinates defined as equation (1)and (2), the upper part of the model atmospnere is equivalent to p-coordinates. The new system of governing equations is obtained as equations (8)-(18). Construction of the finite difference scheme is generally similar as 1, but the difference equations of hydrostatic equations are obtained from differentiating them with respect to time as equations (27)-(28).A combined scheme of the leap-frog method and the time smooth method is employed for the explicit integration.The physical factors of orography, friction, horizontal diffusion and nanadiabatic-heating such as radiation, sensible heating, evaporation, large-scale and cumulus scale condensation are included.The model was tested by using objective analysis and compared with the general σ-coordinates. Finally two examples of 48 hours prediction for winter and summer are given in this paper.