The invention discloses a short address improvement based intelligent substation merging unit configuration method and belongs to the field of substation automation of an electric power system. The short address improvement based intelligent substation merging unit configuration method comprises the steps of generating an SCD (Substation Configuration Description) file of the intelligent substation based on an ICD (IED Capability Description) file of a merging unit by an SCD configuration tool, wherein the short address in the ICD file includes ICD configuration information; enabling the configuration information to correspond to a virtual port number of the short address; parsing the short address in the SCD file by utilizing a merging unit configuration tool and exporting a configuration file of merging unit information; downloading the configuration information to the merging unit by utilizing a merging unit tool so as to finish the configuration process. As the short address improvement based intelligent substation merging unit configuration method is utilized, the problems of excessive merging units and great debugging workload in the intelligent substation are solved.