Superhot geothermal environments in granitic crusts of approximately 400–500 °C are a frontier of geothermal energy. In the development of such environments, there is a concern of a reduction of permeability of fractured granite due to the formation of fine particles of amorphous silica induced by the phase change from subcritical water to supercritical water or superheated steam. However, the formation of silica particles and a resultant reduction in permeability have not been demonstrated to date. Therefore, experiments were conducted on the formation of amorphous silica particles with various combinations of temperature (430–500 °C) and pressure (20–30 MPa), in which the phase change of Si-containing water from liquid to either supercritical fluid or vapor was induced. Amorphous silica nanoparticles occurred under all conditions with smaller particles for higher temperature. The permeability of fractured granite was also observed to decrease significantly within several hours during injection of the particles into rock at 450 °C and 30 MPa under a confining stress of 40 MPa, with slower permeability reduction at a smaller number of particles or in the presence of larger aperture fractures. The present study suggests that the nanoparticles are likely to form and destroy the permeability in superhot geothermal environments, against which countermeasures should be investigated.