A system and a method for hitless clock switching are provided. In the system, a sampling circuitry group samples a primary reference clock signal and a secondary reference clock signal to obtain first and second sampling information, respectively. A phase detector group obtains a phase difference between the primary and secondary reference clock signals with the first and second sampling information. A compensator group adds the phase difference to a phase of the secondary reference clock signal to obtain a backup reference clock signal. When the primary reference clock signal is abnormal or missing, the signal selector determines the backup reference clock signal as a target reference clock signal and sends it to a phase-locked loop. The phase-locked loop performs loop control on the target reference clock signal, thereby implementing hitless switching of reference clock signals.