Although intensive efforts have been devoted to fabricating Ti3C2Tx MXene composites for microwave absorption, it remains a great challenge to achieve excellent MA performance at low loading and thin thickness. Herein, a three-dimensional (3D) lightweight hierarchically structured MnO2/Ti3C2Tx/RGO composite aerogel with abundant heterointerfaces was fabricated via a hydrothermal and chemical reduction self-assembly method. The RGO aerogel embedded with laminated MnO2/Ti3C2Tx provides a lot of heterogeneous interfaces, 3D porous interconnected conductive networks, and reasonable combination of various loss materials for rich interfacial polarization, conductivity loss, multiple reflections and scattering, and good impedance matching. Benefiting from the synergy of different loss mechanisms, the maximum reflection loss (RL) is up to -66.5 dB (>99.9999% energy absorption) at only 10 wt % loading and 2.0 mm thickness, and even at only 1.5 mm thickness, the maximum RL value remains at -36 dB (>99.9% energy absorption). The work provides a promising route to construct 3D hierarchically heterogeneous composite aerogels for efficient MA at thin thickness and low loading.