Nickel cobaltate@polypyrrole composite nanomicrospheres (NiCo2O4@PPy) were successfully synthesized by in situ oxidation polymerization on the surface of NiCo2O4 microspheres with polypyrrole layer as a shell. The impedance matching can be optimized by modulating the amount of polypyrrole, so as to obtain the best wave absorption performance. Furthermore, the full absorption of multiple bands can be realized under different thickness. The absorption mechanism of EMW is specifically analyzed, that is, the appropriate impedance matching and the large dielectric and magnetic losses caused by the electromagnetic synergistic effect generated by the heterogeneous interface of NiCo2O4 and PPy. NiCo2O4@PPy-0.8 achieves remarkable impedance matching in a wide frequency range compared with other samples, thus obtaining superior absorption performance. When the thickness of NiCo2O4@PPy-0.8 is 2.3 mm, the effective absorption bandwidth (EAB, RL exceeding −10 dB) at 10 wt% loading reaches 7.14 GHz (ranging from 10.86 GHz to 18 GHz, covering the whole Ku band), and the minimum reflection loss (RLmin) is −57.85 dB. This work provides an encouraging method for lightweight ultra-wideband electromagnetic wave absorption of multilayer structures based on nickel-cobalate matrix.