In this study, the different effects of nanoparticle aggregates and agglomerates on the mechanical properties of polymer nanocomposites are comprehensively investigated. To this end, a specific strategy, based on the equilibrium between the dispersion and cohesion energies in the mixing stage, is proposed using which the content and size of aggregates/agglomerates can be defined. The aggregated/agglomerated networks are considered to place in constrained volumes (CVs), having co‐continuous morphology. An equivalent box model (EBM), corresponding to the system, is used to predict the tensile modulus of the nanocomposite. Different test results of HDPE nanocomposite samples, containing 1–3 wt.% of surface‐modified silica nanoparticles, prepared by a semi‐industrial single screw extruder, are applied to validate the model. Moreover, other data from the literature are also used to further evaluate the accuracy and capability of the proposed analytical method.