The invention relates to a composite carrier of an alumina-coated molecular sieve, a hydrocracking isomerization catalyst, and a preparation method and application thereof. Firstly, a molecular sieveis subjected to an amino acid pore broadening treatment; then the molecular sieve is sulfonated, the sulfonated molecular sieve is added into an alcohol-water solution containing hexadecyl trimethyl ammonium bromide, an aluminum source and urea are added, and then crystallizing, washing, drying, and roasting are performed to obtain the composite carrier, which has abundant pores and abundant acidic sites, thereby enhancing the hydro-isomerization performance. Pt, Pd, Ni and Co are used as main active metals; Na, K, Be, Mg, Ca, Sr, Cr, Mn, Fe, Cu and Zn are used as auxiliary metals; and the auxiliary metals can enhance the dispersity of the active metals, can selectively cover and inhibit the acidic sites of the molecular sieve, play a key role in hydrogenation activity, and have higher activity in the aspect of preparation of biofuel from long-chain alkane through hydro-isomerization.