A combination of heat pump and humidification-dehumidification (HDH) process is a suitable choice to obtain fresh water for small-scale desalination applications, especially when the solar energy is used as the auxiliary heat source. In this paper, a novel two-stage solar assisted heat pump (SAHP) desalination system based on HDH, in which the humidifiers are connected in parallel, is proposed. A mathematic model is developed to improve the system performance by optimizing the operating parameters such as process air flow rate and cooling seawater flow rate, and it is also validated by the experimental results. Analysis results indicate that there exists an optimal process air flow rate in the desalination system, which 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 m(3)/h and 0.55 m(3)/h, respectively, the maximum fresh water yield is 17.94 kg/h. The corresponding gained-output-ratio (GOR) is 2.02. However, the system performance is constrained by a bottleneck: increasing dehumidifying capacity can result in a reduction in the performance of lower-temperature (LT) humidifier. Consequently, a modified system is then proposed to solve this bottleneck effectively. The maximum fresh water yield can be increased by 16.70% to 20.54 kg/h, and the corresponding maximum GOR is also increased by 18.05% to 2.42.