Two polymers of same functional group were used; one with greater chain flexibility, PA 6.6, and the other with two benzene rings in the main chain, PA 6I‐6T (aPA), to evaluate how the structure influences on the nanoparticle dispersion homogeneity and on dynamic‐mechanical properties. In the aPA nanocomposites, good dispersion and homogeneous distribution were observed for all CNT concentrations. However, PA 6.6 nanocomposites showed agglomerated regions in all formulations. The interfacial energy of the aPA/CNT was five times lower than that of PA6.6/CNT, resulting in greater compatibility in this nanocomposite. An increase of up to 26% was observed with 2.5% of CNT in aPA nanocomposites storage modulus. In the samples with PA 6.6, the increase was at most 5%. Even with greater flexibility of PA 6.6 macromolecules, the π‐π interaction between the aPA aromatic rings and CNTs might be the decisive factor for dispersion improvement and positively influence on the dynamic‐mechanical properties of these nanocomposites. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 48195.