Nanocomposite materials filled with multiwall carbon nanotubes (MWCNTs) having three types of structures, i.e., longer (200 μm), shorter (20–50 μm), and aminated (20–50 μm), are manufactured for microwave absorption (MA) in 11–17 GHz frequency range. Microstructure, dielectric permittivity, direct current (DC) electrical conductivity, and MA properties of the MWCNTs–epoxy nanocomposite were investigated. A correlation has been developed between the structure (aspect ratio and surface functionality) of MWCNTs, electrical conductivity of the composite, and MA (return loss (RL)). E-glass/epoxy composite filled with longer carbon nanotubes (CNTs) has shown higher RL as compared to that of other two nanocomposites. The measurements have shown that the magnitude of RL of microwaves depends strongly on the structure of MWCNTs used in the composite. Furthermore, the effect of synthesis route followed for the manufacturing of nanocomposite on its electrical conductivity and microwave absorbing properties is also investigated; three different approaches were followed to manufacture CNT/epoxy nanocomposites from longer CNTs (200 μm).