The invention belongs to the technical field of medicines and discloses cytarabine 5'-O-amino-acid ester, pharmaceutically acceptable salts thereof and a preparation method thereof. The preparation method comprises the following steps of: slowly dropping carbobenzoxy chloride into a solution formed by cytarabine, sodium bicarbonate and N,N-dimethylacetylamide, and obtaining a compound A after reacting at room temperature; using the compound A and N-butyloxy formoxyl-amino acid as raw materials; adding a reagent to the solution to carry out an esterification reaction to obtain the cytarabine 5'-O-amino-acid ester; and then adding acid to obtain a finished product. The pharmaceutically acceptable salts comprise hydrochlorides, sulfates, formates, acetates, mesylates, propionates, butyrates, p-toluene sulphonates, phosphates, bisulfates, maleates, lactates, carbonates, bicarbonates, malonates, and salts formed with acidic amino acids, and the like. The invention can obviously improve the membrane permeability of the cytarabine so as to improve the bioavailability of the cytarabine.