The invention relates to an intelligent substation secondary virtual terminal diagram-reality consistency detecting method based on a handheld device. CID and SCD files are firstly made consistent, the handheld detection device acquires the CID file of an IED device through an optical fiber interface, and the CID file is directly compared with a CID file which is directly exported from the SCD file so that whether the CID files are consistent or not is determined; the handheld detection device obtains the SCD file from a monitoring background through an internet access, an EXCEL virtual terminal drawing designed by the designing institute serves as a correct standard and is compared with virtual terminal information in an SCD configuration file to confirm whether the SCD configuration file is consistent with the EXCEL virtual terminal drawing designed by the designing institute or not, accordingly whether the SCD configuration file is correct or not is determined, a diagram-reality consistency report is automatically generated, and intelligent substation secondary virtual terminal diagram-reality consistency is full-automatically achieved. By adopting the method, the accuracy can be up to 100%, the time saving rate can be up to 95% or above, the working efficiency is improved, and reliable and safe operation of a power grid is ensured.