The invention relates to a hydro-upgrading catalyst for diesel oil with high content of aromatic hydrocarbons, and a preparation method and application thereof. The catalyst comprises, by weight, 20 to 65% of a composite molecular sieve, 10 to 50% of alumina, 10 to 30% of VIB-group metal (in terms of oxide) and 3 to 8% of VIII-group metal (in terms of oxide), wherein the composite molecular sieve is composed of a small-grain modified Y molecular sieve and a SAPO-11 molecular sieve in a weight ratio of 2: 1 to 10: 1. The invention also discloses a preparation method for the small-grain modified Y molecular sieve. The preparation method comprises the following step: successively subjecting a raw material, i.e., a small-grain high-silica-alumina-ratio NaY molecular sieve with a SiO2/Al2O3 mol ratio of 6.0 to 7.0, to primary ammonium exchanging, primary hydro-thermal treatment, secondary ammonium exchanging, secondary hydro-thermal treatment and primary acid treatment. With the catalyst prepared in the invention, high liquid product yield is obtained, and diesel oil with high content of aromatic hydrocarbons can be used for production of low-sulfur olefin-free high-octane-number gasoline and ultra-low-sulfur clean diesel oil.