In this contribution, the micro- and macro-structure of plasma grown hydrogenated nanocrystalline silicon (nc-Si:H) thin films were followed with respect to substrate temperature (Ts) ranging from 80 °C to 200 °C. nc-Si:H films were deposited by plasma enhanced chemical vapor deposition technique using silane gas highly diluted by hydrogen and high RF power density. Micro-structure analysis was performed with grazing angle X-ray diffraction (GAXRD) and dispersive Raman spectroscopies. Parallelly, morphological properties of the films were investigated via field emission scanning electron microscopy (FE-SEM) by taking both surface and cross-sectional micrographs. GAXRD results suggest the presence of 4–5 nm nanocrystallites with the size almost independent of Ts. The detailed analysis of the Raman spectra reveals one- and two-phonon modes due to amorphous and crystalline silicon (c-Si), where all c-Si related peaks shifted to lower frequencies. Raman nanocrystalline volume fraction is found to be greater than 50% for all Ts; it increases together with the short-range order at elevated Ts. This micro-structural improvement with Ts is considered to be slight when compared to the FE-SEM-observed drastic changes of morphology, particularly the size of large conglomerates (35–250 nm). The behavior of micro- and macro-structure with Ts is correlated well with the previously determined bonding and lateral conductivity measurements. It seems to be the macro-structure that accounts for bonding and electrical properties of nc-Si:H thin films.