Nickel-supported hierarchical zeolite catalysts were prepared through a desilication reassembly process under optimized conditions and applied in one-pot menthol synthesis. In this work, the hierarchical zeolite-supported metal bifunctional catalysts were prepared with the help of desilication re-assembly and wetness impregnation techniques and applied in menthol synthesis via citral hydrogenation. The prepared catalysts were characterized using PXRD, BET, FE-TEM, NH3-TPD, H2-TPR, pyridine adsorption, and ICP-OES techniques. As a result, the physicochemical and acidic properties, such as mesopore surface area, metal dispersion, acidity, catalytic activity, and strong Lewis acid sites of pure microporous ZSM-5/USY zeolites, were significantly improved. Consequently, with the occurrence of superior physicochemical and acidic properties, the Ni/HZ-0.5 M catalyst exhibited outstanding catalytic activity (100% conversion, TOF 7.12 h−1) and menthol selectivity (83%, 4 h) with uniform stability at 100 °C, 1.0 MPa hydrogen. Similarly, the cracking rate decreased with the decrease in Bronsted acid sites.