Nanostructured amorphous carbon thin films deposited by a Low Energy Carbon Cluster Beam Deposition technique have been characterized by Raman spectroscopy and Electron Spin Resonance (ESR). This study focuses on the correlation between carbon cluster structure and sp2 related defects. The ESR spectrum of as prepared and thermally annealed carbon clusters is a single line located near the free electron g-factor. Resonance lines were accurately fitted by a single line symmetric and narrow Lorentzian line. The resonance line parameters (line position, line amplitude, and line width) were found to be extremely sensitive to the thermal treatment of the as deposited samples. The paramagnetic centres are randomly distributed and correlated with the nanosized nature of the investigated system. The absence of the resonance line asymmetry, typical for the ESR spectra of conducting carbaceneous materials, confirms the small size of carbon nanoclusters and indicates poor electrical contacts between them. The resonance line parameters (position, intensity, and width) are not affected by the orientation of the carbon cluster film relative to the direction of the external magnetic field. The evolution of the ESR signal upon thermal treatments is sensitive to the increase of the sp2 average domain size as revealed by Raman spectroscopy. The Raman spectrum of as obtained and thermally annealed carbon clusters, in the domain 1000 cm−1 to 2000 cm−1 shows two Lorentzian lines located at 1300 cm−1 and 1550 cm−1 representing the D and G bands. The position and amplitude of these lines were found to be affected by thermal annealing.