Based on lean thinking of industrial engineering, this paper studies goods handling systems of logistics enterprises by taking the W warehouse in J logistics company as an example. Through field visits, observation, and operation，problems in site layout, unlocking registration procedures, and goods handling process when goods arrive at the warehouse for transshipment are found. Based on the theories and methods of layout optimization, two-hand operation analysis and process program analysis, this paper proposes a reasonable and feasible optimization scheme to reduce labor cost and time cost, so as to improve the efficiency of goods handling system.