A combination of heat pump and humidification-dehumidification (HDH) process is an excellent choice to provide drinkable water for small-scale desalination applications, especially when the solar energy is used as the auxiliary heat source. In this paper, a two-stage solar assisted heat pump desalination system based on HDH is proposed, which is beneficial for improving the performance of internal heat recovery. A mathematic model is developed to optimize the operating parameters such as process air flow rate and cooling seawater flow rate, and it is also validated by the experimental results. Simulation results show that there exists an optimal process air flow rate in the desalination system, and it does not vary with the hot seawater flow rate. However, it will be increased with the increase of cooling seawater flow rate. When the flow rates of process air and cooling seawater are 350 m³/h and 0.55 m³/h, respectively, the maximum fresh water yield is 17.94 kg/h.