It is an effective strategy that constructing composites with a multi-dimensional structure synergistically enhance their electromagnetic (EM) wave absorbing performance. Herein, a high-efficiency EM wave absorber of Mo2C/C nanoclusters uniformly encapsulated in rGO nanosheets (Mo2C/C-rGO) was prepared by a combination of the directing freeze-dry and subsequently carbothermal reaction method. Mo2C/C was in-situ induced from spherical phosphomolybdic acid/polypyrrole (PMo12/PPy) to result in a unique cluster-like microstructure. Abundant heterogeneous interfaces endowed the Mo2C/C-rGO composites with excellent EM wave absorption performance at a low filling ratio of 5 wt%. The minimum reflection loss (RL) value was −49.3 dB at 1.38 mm and the maximum effective absorption bandwidth (EAB, RL<-10 dB) was 5.12 GHz at 1.60 mm. The excellent performance was owing to the lamellar structure and abundant heterogeneous interfaces in Mo2C/C-rGO, lengthening the transmission path of the incident wave, as well as resulting in high conduction loss and interfacial polarization loss. This universal strategy would be extended to other absorbers with multi-interface structures for lightweight and broadband EM wave absorption.