Magnetic properties of solvent-free crystals of the endohedral Sc@C82 are investigated by SQUID and X-ray powder diffraction. We find that the crystal is a paramagnet and the magnetic susceptibility decreases from 150 K with evidence of antiferromagnetic-like interactions by slow cooling. X-ray crystal analysis reveals the presence of a phase transition at 150 K, which is attributed to an orientational ordering transition of the fullerene molecules. At low temperatures we find a magnetic metastable state that can be controlled by the cooling rate. The metastable state can be formed by rapid cooling. The direction of Sc@C82 molecular axis in the crystals is disordered in the metastable state, and the susceptibility is higher than that in the slow cooling case at low temperature.