A theoretical model is developed for the dynamic characterization of hybrid polymer-based solar cells (HPSCs) based on vertically aligned ZnO/CdS-core/shell nanorod arrays (ZC-NAs) by intensity modulated photocurrent spectroscopy (IMPS). The model describes the effects of CdS shell formation on charge generation and transport dynamics. Particularly, an analytical expression for the ineffective polymer phase model in nanoarray solar cells is developed and introduced into IMPS model for the first time. The main expectations of the IMPS model are confirmed by the experimental data of the polymer/ZC-NA cells with the CdS shell thickness (L) of 3–8 nm. It is shown that the contributions from CdS absorption (f1) and polymer absorption (f2) to charge generation are determined by the core/shell nanoarray structure and the intrinsic polymer property, while the optimal CdS shell thickness (Lopt) depends on the interspacing between ZnO core nanorods and the exciton diffusion length of the polymer. The photocurrent generation is dominantly the competitive results of f1 and f2 contributions subjected to the change in L, with the polymer as a dominant absorption material. Fittings of the measured IMPS responses to the IMPS model reveal that the L-dependence of photocurrent generation dominantly originates from f1, f2, and the polymer exciton dissociation rate S at the polymer/CdS interface. Moreover, the first-order rate constants for the surface defects to trap and detrap the injected electrons in ZnO core nanorods are found to decrease with CdS shell growth and become saturated at Lopt. Furthermore, it is demonstrated that the effective electron diffusion coefficient De in the ZnO nanorods reaches a peak value at Lopt as the result of the largest photogenerated electron density in conduction band. Those results provide a guide to the design of efficient HPSCs based on the core/shell nanoarrays with complementary properties.