The morphology, specific surface area, structure, and phase composition of natural zeolite powder from the Tokai deposit which underwent mechanical treatment in a planetary mill was studied using the following methods: scanning electron microscopy (SEM), X-ray structural analysis, Brunauer–Emmett–Teller (BET) method, laser diffraction, and elemental analysis. The identification of natural zeolite X-ray patterns showed that the powder consisted of seven phases with different contents of minerals: smectite, quartz, cristobalite, clinoptilolite, illite, orthoclase, and calcite. Initially, the average size of the zeolite particles was 27 μm; after the treatment for 20 min, it was 5.5 μm; and after 600 min, it was 28 μm. Moreover, most of the particles lost their initial shape during the mechanical activation and acquired a spherical shape. It was shown that, during the first 60 min of mechanical treatment in the planetary mill, powder particles were ground, and the specific surface area increased to 33 m2/g. The further mechanical activation was determined by agglomeration of particles and a decrease in the specific surface area. The X-ray structural analysis showed that the studied powder consisted of four phases: hexagonal, monoclinic, orthorhombic, and tetragonal modifications. Mechanical treatment of natural zeolite led to the decrease in the coherent scattering regions and to the growth of microdistortions of the crystal lattice. It was shown that the continuous mechanical effect on zeolite led to the increase in the amount of an amorphous phase in the powder from 13 to 52%. The changes in the specific surface area determined by the BET method and calculated from the coherent scattering region (CSR) had the same character, and the phase composition determined the specific surface area of natural zeolite.