Motivated by the unique structure and outstanding properties of graphene, three-dimensional (3D) graphene-based polymer nanocomposites (3D-GPNCs) are considered as new generation materials for various multi-functional applications. This review presents an overview of the preparation, properties and applications of 3D-GPNCs. Three main approaches for fabricating 3D-GPNCs, namely 3D graphene based template, polymer particle/foam template, and organic molecule cross-linked graphene, are introduced. A thorough investigation and comparison of the mechanical, electrical and thermal properties of 3D-GPNCs are performed and discussed to understand their structure-property relationship. Various potential applications of 3D-GPNCs, including energy storage and conversion, electromagnetic interference shielding, oil/water separation, and sensors, are reviewed. Finally, the current challenges and outlook of these emerging 3D-GPNC materials are also discussed.