The utility model discloses a negative sequence compensation system in electrified railways. The negative sequence compensation system comprises a signal acquisition controller, a magnetically-controlled reactor, and a capacitor branch. The magnetically-controlled reactor is connected with the high-voltage side of a power grid. The capacitor branch is connected with the low-voltage side of the power grid. The signal acquisition controller is connected with the magnetically-controlled reactor and the capacitor branch. According to the active power and the reactive power among the three phases of the power grid, the signal acquisition controller calculates the value of capacity required to be compensated among the three phases of the power grid. And according to a calculated result, the signal acquisition controller generates a control signal for controlling the capacitor branch to provide reactive power and the magnetically-controlled reactor to output compensation capacity. The negative sequence compensation system is capable of reducing the installed capacity and the floor space of a compensation system while achieving negative sequence compensation of electrified railways.