The invention provides a relay protection online safety margin evaluation system. The system includes a master station end device installed in a dispatch center and a plurality of sub-station end devices installed in a transformer substation; the master station end device and the sub-station end devices are used for relay protection online safety margin evaluation; the master station end device includes a protection safety margin evaluation module, a data acquisition and processing module, a human-computer interaction module and a public data area; and each sub-station end device includes a protection safety margin evaluation sub module, a data acquisition and processing sub module, a human-computer interaction sub module and a public data sub area. Compared with relay protection online setting or online check, the system can accurately judge whether a protection constant value meets the requirements of the current operation mode of a power grid for protection selectivity and sensitivity and can assist in effectively eliminating the defect that the accuracy of relay protection online setting and online check results is influenced by the accuracy of power grid power flow, power grid parameters and a short-circuiting calculation model.