The invention belongs to a multilevel processing method of waste water and a processing system thereof, and in particular discloses a processing method and a processing system for acidic waste water containing heavy metals. The invention comprises the following steps of: mixing carbon powder and scrap iron, adding modified zeolite, and placing the mixture into an inner electrolytic cell; conveying preprocessed waste water into the inner electrolytic cell, and reacting for 10 to 30 minutes under aeration condition; enabling outlet water to enter an electrochemical reaction cell directly, wherein the space between polar plates in the cell is from 0.6 to 1.4 cm, and reacting for 5 seconds to 5 minutes; and precipitating the outlet water, and separating solid from liquid. The processing system comprises a regulation cell, the inner electrolytic cell, the electrochemical reaction cell, a precipitating cell and a filtering cell which are sequentially connected, wherein the inner electrolytic cell is internally provided with a reaction bed, filter materials consisting of zeolite, carbon powder and scrap iron are filled in the reaction bed, an electrochemical reactor is installed in the electrochemical reaction cell, and a surface film filter is arranged in the filtering cell. The processing method has the advantages of wide application range, stable operation, good processing effect, low processing cost, environment protection, no pollution, and the like.