The invention discloses a modified molecular sieve-based noble metal catalyst for deep hydrodearomatization of diesel and the preparation method thereof. The catalyst is suitable for hydrodearomatization of the FCC diesel, particularly suitable for deep hydrodearomatization of diesel after hydro-upgrading of the FCC diesel. The dearomatized diesel can be used as a blend component of high-quality diesel. The catalyst contains modified HY molecular sieve as carriers and noble metals such as Pt, Pd and Ir as active components. The industrialized HY molecular sieve is modified to have microporous-mesoporous structure, and the carrier has medium acidity and is doped with Cr, Zn, Sn and Mo oxides of the active components with ring-opening selectivity, so that the inventive catalyst is characterized in deep cracking inhibition and ring-opening selection. The catalyst is used in the deep hydrodearomatization of the second stage in the two-stage hydro-upgrading of diesel.