Growing graphene on SiC thin films on Si is a cheaper alternative to the growth on bulk SiC, and for this reason it has been recently intensively investigated. Here we study the effect of hydrogen intercalation on epitaxial graphene obtained by high temperature annealing on 3C-SiC/Si(111) in ultra-high vacuum. By using a combination of core-level photoelectron spectroscopy, low energy electron diffraction, and near-edge x-ray absorption fine structure (NEXAFS) we find that hydrogen saturates the Si atoms at the topmost layer of the substrate, leading to free-standing graphene on 3C-SiC/Si(111). The intercalated hydrogen fully desorbs after heating the sample at 850 °C and the buffer layer appears again, similar to what has been reported for bulk SiC. However, the NEXAFS analysis sheds new light on the effect of hydrogen intercalation, showing an improvement of graphene's flatness after annealing in atomic H at 600 °C. These results provide new insight into free-standing graphene fabrication on SiC/Si thin films.