A comparative study of morphology and properties of poly(butylene terephthalate)/carbon nanotubes (PBT/CNTs) nanocomposites with non-reactive and reactive elastomers was comprehensively performed. The carboxyl-functionalized CNTs showed uniform dispersion and formed an interconnecting network structure at relatively high content in both nanocomposites. However, the location of CNTs and the resulting morphology were different in these two nanocomposites as a result of chemical interactions between the reactive elastomer and functionalized CNTs. Evaluation of mechanical performance demonstrated that CNTs enhanced the tensile strength and modulus of both nanocomposites. However, the incorporation of CNTs did not enhance the toughness of the two nanocomposites, although elastomer particle size decreased in the nanocomposites with the non-reactive elastomer. The volume resistivity of both nanocomposites was extremely reduced with CNTs, but the volume resistivity of the nanocomposites with the non-reactive elastomer decreased more due to the more significant volume exclusion effect of the non-reactive elastomer. With the addition of a reactive elastomer and CNTs, electrical conductive PBT nanocomposites with balanced toughness-rigidity were obtained.