The invention belongs to the technical field of railway construction operation protection, and particularly relates to an upper operation safety protection system which comprises an administrator terminal, an indoor liaison terminal, an outdoor protector terminal, a field operating personnel positioner and an upper operation protection server. The invention also relates to an upper operation safety protection method. According to the invention, a Beidou differential positioning technology and TDCS station yard information are adopted, the upper operation protection server acquires the accurateposition of a field operating personnel, the accurate position of a train, station yard signal display, route information and the like in real time, safety protection information of the field operating personnel is formed after comprehensive processing, and route forecast is automatically reported to the indoor liaison terminal and the outdoor protector terminal to remind the field operating personnel not to interfere with an open route.