Disclosed herein is a method for diagnosing and controlling a two-step exhaust variable valve lift (VVL) system, including: a controlling device acquiring an operation state signal of a vehicle; when the vehicle is in the over-run state, the controlling device outputting a mode conversion signal of the two-step exhaust VVL system; an air mass sensor measuring an air mass entering an engine, and the controlling device comparing a predetermined prediction value of the air mass with the measured air mass; when a difference of the compared air mass corresponds to a predetermined mode conversion comparing amount, the controlling device determining that a mode conversion of the two-step exhaust VVL system is completed; and when the difference of the compared air mass does not correspond to the mode conversion comparing amount, the controlling device determining that the two-step exhaust VVL system is faulty and outputting a result thereof.