The invention discloses a bus protection system and method based on voltage phase locking networked sampling. The system comprises a PT merging unit, a plurality of spaced merging units, an interchanger and a bus protection device, the bus protection device comprises a FPGA, a message processor and a protection processor, and the method comprises the following steps of recording the arrival time of each frame of a sampling value message in real time, analyzing the sampling value messages, tracking the sending frequency of sampling values of the merging units, measuring network transmission extra delay errors, synchronizing the interpolation of the sampling values and performing relay protection on a bus. The bus is protected based on voltage phase locking networked sampling, the sampling values are output by the interchanger, the sampling value messages are output in a unified mode, failure analysis of a power system is facilitated, the number of the spaced merging units is set according to the requirement of a protected bus, the number is set flexibly, the engineering implementation is flexible, the synchronization logic and bus protection logic are relatively independent, and the system and method are suitable for being popularized and used in multiple areas.