The invention discloses a handheld nuclear phase instrument and nuclear phase method applied to an intelligent substation, belongs to the technical field of intelligent substation engineering protection system nuclear phase, and particularly relates to the handheld nuclear phase instrument and nuclear phase method applied to the intelligent substation. The invention provides the handheld nuclear phase instrument and nuclear phase method applied to the intelligent substation, and a nuclear phase problem of the intelligent substation can be effectively solved. The handheld nuclear phase instrument applied to the intelligent substation comprises a handheld nuclear phase instrument body and is characterized in that the handheld nuclear phase instrument body is provided with a touch display screen, a switch quantity interface, a light serial port, a light Ethernet port, a TF card slot, an indication lamp, an analog quantity acquisition port and keys. The handheld nuclear phase instrument body is internally provided with an ARM processor, a power management part, an FPGA and an A/D conversion module. The ARM processor is connected to the touch display screen, the switch quantity interface, the TF card slot, the indication lamp, the keys, the power management part and an FPGA output port.