A mathematical model is presented to analyze the performance of a counter-current solar desalination system. Besides, the heat transfer equations, the mass transfer is also considered to improve the model precision. A new approach is used for analyzing the radiative heat transfer in these systems. A low enough value for feed flow rate, a moderate value for glass temperature, taking the advantage of high flux at the appropriate time and appropriate insulation of the floor could effectively increase productivity. The system length is also a significant parameter. The model can be sufficiently extended for other continuous solar desalination systems.