A method of two-step variable valve lift (VVL) malfunction avoidance learning control may include: in a two-step VVL system which is operated with a main lift and a secondary lift, verifying, by an electronic control unit (ECU), an operation avoidance area based on locking of a lock pin of a cam follower ; performing VVL operation learning, in which a failure of occurrence of the second lift is determined on the basis of a locking failure of the cam follower due to an initially set value of the operation avoidance area; and reflecting the operation avoidance area to the two-step VVL system with a corrected set value which is obtained through the VVL operation learning.