Transition metal molybdate (RMoO4) has been extensively studied in optics, electricity and catalysis due to its low cost and multivalent Mo atoms, while its poor electrical conductivity limits its application in electromagnetic wave absorption (EMA). Compounding molybdate with conductive materials is an effective way to improve its electrical conductivity. In this work, a homogeneous coating on the molybdate surface was achieved by utilizing a pyrrole oxidation polymerization mechanism, and then stabilized composites of Molybdate@Carbon (RMoO4@C) were obtained by high-temperature pyrolysis. The EMA properties of the nanocomposites were tuned by substituting the species of transition metal elements (RMoO4@C, R=Fe, Co, Cu). Among them, Fe2(MoO4)3@C has a minimum reflection loss of −60.62 dB at an ultra-low thickness of 1.7 mm, and the effective absorption bandwidth (EAB) can reach 4.75 GHz at 3.00 mm. This work expands the range of applications for molybdate and provides a new material basis for building high-performance EMA materials.