Photothermal-assisted water purification is a promising and sustainable scheme to the global clean water crisis. In this work, we report a custom-tailored bilayer photothermal aerogel to integrate multiple purification mechanisms through a cost-effective route. It is composed of a bottom layer of polyethylenimine-modified chitosan (PEI-CS) and an upper layer of CuS nanoflower/reduced graphene oxide (CuS/rGO) composites. Benefiting from the vertically aligned microchannels, PEI-CS scaffold exhibits rapid capillary pumping characteristics for water transport, and absorbs heavy metal ions by forming chelating bonds with excess hydroxyl and amino groups. With a facile spraying fabrication, the spatial distribution of CuS/rGO is rationally controlled to improve the upper thermal localization. More practically, the harnessed solar energy can be utilized by CuS/rGO nanoheterostructure with pronounced charge separation for photocatalytic degradation in parallel to efficient vapor generation. The low-cost raw materials, scalable fabrication, and multifunctionality make the bilayer aerogel be potentially applied in wastewater remediation.