The invention provides an instantaneous frequency measuring method and system. The method includes that a polarization modulator performs polarization modulation on to-be-detected microwave signals and a first adjustable light source as well as a second adjustable light source; a polarization beam splitter divides the to-be-detected microwave signals to first branch optical signals and second branch optical signals; a first polarization controller and a first analyzer perform phase modulation on the first branch optical signals; a second polarization controller and a second analyzer performs intensity modulation on the second branch optical signals. A dispersion element is utilized for performing dispersion attenuation on the two branch optical signals. A first photoelectric detector converts the first branch optical signals subjected to dispersion attenuation to first branch electric signals. A second photoelectric detector converts the second branch optical signals subjected to dispersion attenuation to second branch electric signals. A digital processing unit obtains the instantaneous frequency of the to-be-detected microwave signals according to the input signals of the photoelectric detectors. The method and system provided by the invention can meet requirements for measurement range and measurement precision in instantaneous frequency measurement.