The present invention provides a method and a system for preparing fuel using high-acid-value biological grease, which can be processed through triple deoxidization steps, i.e., thermal cracking deoxygenation-catalytic cracking deoxygenation-catalytic hydrodeoxygenation. By use of the method and system of the invention, the raw material of the high-acid-value biological grease can be gradually deoxidized to reduce the acid value and thereby prepare a clean fuel with equivalent fuel components as those obtained from crude oil refining or direct hydrodeoxygenation for biological grease.