Single crystals of FeTe0.65Se0.35, with the onset of critical temperature (Tc) at 14 K, were hydrogenated for 10–90 hours at various temperatures, ranging from 20 to 250 oC. It is shown that tetragonal matrix becomes unstable and crystal symmetry is reduced for the crystals hydrogenated already at 200 oC despite that molecular impurities do not change matrix symmetry, unless the material is not destroyed under hydrogenation at 250 oC. Bulk Tc, takenat the middle of the transition, equal to about 12–13 K for the as-grown FeTe0.65Se0.35, increases by 1–2 K. The critical current density determined in magnetic field range of 0–70 kOe increases 4–30 times as a result of hydrogenation at 200 oC for 10 h. Electron paramagnetic resonance studies confirmed higher value of the bulk Tc for hydrogenated crystals. Thermal diffusion of hydrogen leads to substantial structural changes, causes degeneration of crystal quality, and significantly affects superconducting properties. A strong correlation was observed between the structural changes and changes in the parameters of the superconducting state for the hydrogenated crystals.