A study aimed at investigating the process of formation of hybrid nanocomposites consisting of a thin polyimide layer containing copper nanoparticles of varying sizes (3-10 nm in diameter) is described. In this system, precursor layers in which copper ions are fully or modestly doped in a chemically modified polyimide matrix are annealed in a hydrogen atmosphere at a constant heating rate. Reduction behavior of doped copper ions and changes in the chemical structure of the matrix film were characterized by inductively coupled plasma atomic emission spectroscopy and Fourier transform infrared spectroscopy, respectively. The results revealed that there is a strong correlation between both the process of reduction to form copper nanoparticles and the dehydration reaction of the matrix that forms heterocyclic imide rings (re-imidization), depending on the initial loading of copper ions. Transmission electron microscopy coupled with nanobeam energy-dispersive X-ray analysis was utilized to observe that upon annealing at a relatively high temperature, copper clusters and nanoparticles are initially formed, and further annealing lead to growth of larger monodispersed particles, which could be attributed to diffusion-controlled aggregative growth at the expense of clusters and smaller particles. These experiments provided important implications for the microstructural tuning of the hybrid nanocomposites based on approaches using these ion-doped precursor resins.