Previously available synthesis of crumpled graphene is always based on external substrates or triggers, and it is still a daunting challenge to construct three-dimensional (3D) porous graphene aerogels with crumpled nanosheets without additional corrugation-inducers. Here, we report a novel and facile method to fabricate crumpled dispersive nanosheets in water directly by tuning oxygen clusters on graphene oxide itself through general alkali-treatment at 70 °C. Given this, 3D graphene aerogel with crumpled nanosheets has been successfully constructed in aqueous via a common sol-gel process. In this kind of 3D architecture, the self-restacking of graphene nanosheets is thoroughly inhibited, and abundant diffusion paths and voids are created. The thus fabricated crumpled aerogel exhibits high elasticity and hydrophobicity with superior absorption capacity of organic pollutants, which is 224%–406% higher than that of conventional graphene aerogels assembled by flat and stiff plates, outperforming most of the pioneering reported graphene aerogels synthesized by sol-gel method. Intriguingly, this architecture also presents excellent recyclability. The suggested facile fabrication of crumpled aerogel with attractive 3D configuration opens a door to promote the performance of graphene-based devices by tuning oxygen clusters and graphitic domains on nanosheets for specific energy storage and sensors applications.