The rational design of structure and regulation of composition in micro/nano-scale is of great significance for broadband absorbing properties of lightweight aerogels. Herein, the controllable dual phase Mo2C/MoO2-decorated rGO aerogels are prepared by designing the Mo-rGO precursor, which possesses heterostructure interfaces and three-dimensional structures. The dual-phase of Mo2C/MoO2 was controlled and nanoparticles were dispersed on the surface of graphene. The interconnected rGO sheets construct continuous network for electron transport, which facilitates conduction loss and multiple reflections inside the aerogel. The Mo2C/MoO2 nanoparticles decorated on rGO sheets contribute sufficient interfacial and dipole polarization, and improve the impedance matching and strengthen the loss capacity of electromagnetic waves. The as-prepared Mo2C/MoO2/rGO aerogel exhibits considerable electromagnetic wave absorption performance with a minimum reflection loss of −42.1 dB at 12.5 GHz and an effective absorption bandwidth of 5.6 GHz (10.6–16.2 GHz) at a thin thickness of 2.2 mm with a low density of 9.8 mg·cm−3. This Mo2C/MoO2/rGO aerogel would be a promising material for electromagnetic wave absorption in wide application fields, and it also provides a universal idea for constructing low-density broadband microwave absorption material by structural and composition engineering.