In this research, the graphene was grown directly on the Si(100) surface at 600 °C temperature using an anode layer ion source. The sacrificial catalytic cobalt interlayer assisted hydrocarbon ion beam synthesis was applied. Overall, two synthesis process modifications with a single-step graphene growth at elevated temperature and two-step synthesis, including graphite-like carbon growth on a catalytic Co film and subsequent annealing at elevated temperature, were applied. The growth of the graphene was confirmed by Raman scattering spectroscopy and X-ray photoelectron spectroscopy. The atomic force microscopy and scanning electron microscopy were used to study samples’ surface morphology. The temperature, hydrocarbon ion beam energy, and catalytic Co film thickness effects on the structure and thickness of the graphene were investigated. The graphene growth on Si(100) by two-step synthesis was beneficial due to the continuous and homogeneous graphene film formation. The observed results were explained by peculiarities of the thermally, ion beam, and catalytic metal activated hydrocarbon species dissociation. The changes of the cobalt grain size, Co film roughness, and dewetting were taken into account.