The present disclosure provides a method for manufacturing a three-dimensional semiconductor memory device. In the method, a storage array is divided into a plurality of storage sub-arrays. As a result, a respective via of each storage sub-array can be etched respectively, which is different from the prior art, where a via for a bottom electrode of a plurality of layers of resistive cells is etched at one time. The vias are filled with metal so that storage sub-arrays are connected with each other. The method for manufacturing the three-dimensional semiconductor memory device according to the present disclosure can substantially reduce process complexity and difficulty of etching process in high-density integration, and also improve a number of layers of the resistive cells integrated in the storage array.