In this study, a three-dimensional (3D) micro-flower like morphology aluminum-doped molybdenum disulfide/reduced graphene oxide (Al@MoS2/rGO) nanohybrids have been developed using a simple and sensitive hydrothermal approach. Their electromagnetic (EM) parameters (permittivity, permeability) and microwave shielding parameters (S11, S12) have been analyzed and reported for the first time in the microwave frequency range of 8.0–12.0 GHz. It is interesting to note that the electrical conductivity of the nanohybrids increases with the doping concentration of Al-ions, whereas skin-depth has a reverse trend. The 12% Al@MoS2/rGO nanohybrid shows a higher total electromagnetic interference shielding effectiveness (EMI SE) value about SET ~33.38 dB, whereas undoped MoS2/rGO nanohybrid exhibits a lower value around ~17.07 dB at the same thin thickness. The higher doping concentration of Al-ion creates lattice distortion and crystal defects with high charge carrier mobility between multiple interfaces and at defective sites. Hence, the Al-doping into MoS2 lattice supported on the rGO surface can greatly enhance EM wave absorption and EMI SE value. The present work suggests that the 12% Al@MoS2/rGO nanohybrid can be treated as a good microwave absorbing and shielding material and useful in various techno-commercial devices. Display omitted •Al-doped MoS2/rGO nanohybrids were synthesized by a simple and sensitive hydrothermal approach.•First-time report Al-doped MoS2/rGO nanohybrids for electromagnetic wave shielding material.•Most of the incoming EM energy attenuated and dissipated inside the 12% Al-doped MoS2/rGO nanohybrid.•Al-ions created more lattice distortion and charge carrier mobility at multi-interfaces or defective sites.•Higher AC electrical conductivity and EMI SE values were achieved by 12% Al-doped MoS2/rGO nanohybrid.