A logistics auditing system and method are disclosed. The logistics auditing method is applicable to an enterprise resource planning (ERP) system stored with logistics data and a customs system stored with customs data. The method first establishes a correspondence data table listing a correspondence relation between the logistics data and the customs data, then inputs logistics data of goods ready to be audited, captures corresponding goods quantity information according to the logistics data and reads customs quantity information corresponding to the customs data in accordance with the correspondence data table, compares the material quantity with the customs quantity, and outputs alarm messages when the material quantity is determined to be different from the customs quantity. Therefore, an enterprise is allowed to monitor a customs bonded/logistics process, and the efficiency of the logistics auditing process is greatly improved.
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