The morphological features of carbon nanotube (CNT) polymer composites and their influence on the effective modulus are evaluated. The considered features include bundle formation from the helical sub‐bundles made of individual CNTs. The formation of bundles is considered as a result of agglomeration of individual nanotubes above and below onset of percolation and is related to electrical conductivity. The proposed geometrical model yields a bundle diameter that agrees closely with that of the experimentally measured by voltage‐contrast method and scanning electron microscopy analysis of polyimide nanocomposites. The proposed micromechanical analytical model includes the helical structure of a bundle and provides close agreement of the effective Young's modulus of nanocomposite over a wide range of CNT content. It is shown that considering the helical structure of CNT bundles and its effect on bundle modulus is vital for predicting the effective modulus of CNT‐polymer nanocomposite.