The disclosure relates to a data transferring method based on a protection and control system for an intelligent substation. Merging unit and intelligent terminal integrated devices for all bays in an intelligent substation are respectively accessed to corresponding transport ports of an FPGA access chip of an intelligent power server. The method includes: in a reception period, messages are read from a reception buffer clip by a real-time business central processor, subjected to a process and then written into the reception buffer clip; in a transmission period, the real-time business central processor issues indication information to the FPGA access chip, causing the chip to generate messages according to the indication information and write the messages into a transmission buffer.