In this paper, a reconfigurable transparent metamaterial absorber consisting of a double-layer indium tin oxide (ITO) complementary resonant structure with a structural water-based substrate is proposed. The double-layer resonant pattern gives rise to two stable resonant peaks, and the loading of the water-based substrate can enhance the microwave absorption of the overall structure. By adjusting the thickness of the water layer in the substrate, the microwave absorption performance of the structure can be switched between dual-band and ultra-broadband, with more than 90% efficient microwave absorption covering the frequency range of 6.1 GHz-35.2 GHz. The absorption mechanism is revealed by analyzing the structure surface current as well as the equivalent dielectric constant. We also experimentally verified its microwave absorption and optical transparency properties. Due to its excellent tunable microwave absorption performance and high optical transparency, the proposed absorber has a large application value in stealth devices and optical windows.