Hydrophobic clinoptilolite (CP) was successfully synthesized via a silanization method using methyltriethoxysilane (MTS) or diethoxydimethylsilane (DMTS) as silane coupling agents. The structural and textural properties of the resultant hydrophobic CP were characterized using various methods. The effect of the amount of MTS or DMTS additive on the induction (nucleation) and growth of CP were also investigated, and the apparent activation energy values for induction and growth periods were calculated, suggesting that the induction period is kinetically controlled, while the rapid growth process is thermodynamically controlled. Meanwhile, DMTS modification enhanced the hydrophobicity of CP compared with its MTS-modified counterpart and pure CP. Finally, various ZnO-supported CPs were used as photocatalysts for the removal of crystal violet from aqueous solution, demonstrating that ZnO/hydrophobic CP has the largest adsorption capacity and best removal performance. These results suggest that hydrophobic CP, as an adsorbent or support, has the most potential for applications in separation and catalysis.