The low tolerance of zeolite in hot liquid water (HLW) could induce crystalline structure destruction and decrease the catalytic activity in aqueous system. Herein, we report modification on the zeolite external surface using organosilane to enhance the hydrophobicity. Pristine NaY was synthesized with a Si/Al ratio of 2.314. HY parent was prepared by ion exchange of NaY zeolite in ammonium chloride solution 0.1 M. External surface of HY zeolite was modified with 3-Aminopropyltriethoxysilane (APTES-HY). The structural stability of HY parent and modified HY after exposure to HLW was investigated at various times (0.5, 1, 2, 4, 10, and 72 h) at 200 °C. The modification with organosilane led to enhanced hydrophobicity and stability in the biphasic system. It was confirmed by XRD and SEM characterizations where the crystallinity and morphology of the treated APTES-HY were more preserved compared to the treated HY parent. XRF characterization showed that the ratio of Si/Al decreased as the time of HLW treatment increased. The decreasing trend of Si/Al ratio might be due to the hydrolysis of Si4+ species from zeolite framework. TGA characterization supports that organic compound protects the external surface of zeolite from degradation in a HLW environment. These studies are expected to upgrade the applications of hydrophobic zeolite as a catalyst in biomass conversion.