The invention discloses a frequency locking system and method based on the Rydberg electromagnetic induction transparent signal. The system includes a probe light source, a coupling light source, a rubidium vapor cell, a photodetector, a sinusoidal signal source, a signal amplifier, a lock-in amplifier and a proportional-integral-integral controller; and the frequency locking method uses a coupledlight source to scan the frequency of the coupled light passing through the rubidium vapor cell to obtain a Rydberg electromagnetic induction transparent signal, and adopts an alternating magnetic field to modulate the atomic energy level to achieve the frequency modulation of the Rydberg electromagnetic induction transparent signal so as to obtain the differential signal of the Rydberg electromagnetic induction transparent signal, namely the error signals required by frequency locking, and the frequency locking for the coupled light laser is performed. The system and method provided by the invention are wide in application range, narrow in line width, simple and stable in structure, low in environmental requirement and low in cost, and are suitable for development of portable systems.