The paper presents a wind–photovoltaic-thermal hybrid-driven two-stage humidification and dehumidification desalination system for remote island regions lacking access to electricity and freshwater resources. By conducting an analysis of the wind and solar energy resources at the experimental site, a suitable wind power station and photovoltaic power station are constructed. The performance of the wind–solar complementary power generation system is then evaluated based on factors such as output power, seawater desalination load power, battery compensation output, system energy consumption, and water production costs. A variable step gradient disturbance method based on the power–duty ratio is proposed for tracking the maximum power point (MPPT) of wind power generation. The output power of the photovoltaic power generation system is optimized, employing a fuzzy logic control (FLC) method to track the MPPT of photovoltaic power generation. This approach effectively addresses the issues of slow speed and low accuracy encountered by traditional MPPT algorithms in tracking the maximum power point (MPP) of both photovoltaic and wind power generations. In order to ensure that the desalination system can operate stably under different weather conditions, eight working modes are designed, and a programmable logic controller (PLC) is used to control the system, which provides a guarantee for stable water production. Experimental results demonstrate that the system exhibits stable performance, achieving a maximum water output of 80.63 Kg/h and daily water yield is 751.32 Kg, the cost of desalination equipment is 1.4892 USD/t.