The invention discloses a fault diagnosis method and a fault diagnosis system based on secondary loop information. The method comprises the following steps of acquiring secondary loop alarm information; determining a plurality of pieces of secondary equipment to be diagnosed corresponding to the secondary loop alarm information; acquiring the topological relation between the secondary equipment and primary equipment; according to the topological relation between the secondary equipment and primary equipment, determining the primary equipment corresponding to the secondary equipment to be diagnosed; acquiring the state information of the primary equipment; and according to the state information, selecting from the secondary equipment to be diagnosed, and determining the secondary equipment which has a fault actually, or determining the primary equipment which has a fault actually. By the method or the system, the precision of diagnosis on the fault information of the secondary loop can be improved, and error diagnosis is prevented.