Disclosed is a multi-wavelength locking method for a wavelength division multiplexing (WDM) optical communication network, and in particular, a multi-wavelength locking method and apparatus for a WDM optical communication system that can lock wavelengths of optical signals by producing pilot tones by applying a sine-wave current to a plurality of transmission lasers having different wavelengths, passing the optical signal through a Fabry-Perot etalon filter, and then Fourier-transforming the filtered optical signal. The multi-wavelength locking method includes frequency-modulating an optical signal by applying a small and specified sine-wave current to a bias current for driving WDM lasers, detecting pilot tones produced after filtering the optical signal through a filtering section and converting the detected signal into a digital signal by performing a sampling of the detected signal, detecting a magnitude and phase of the pilot tones by performing a fast Fourier transform, providing Fourier-transformed data as a first derivative signal of the filtering section, and locking an operation wavelength of WDM channels by controlling the temperature or current if resonance frequencies of the filtering section coincide with respective standard frequency.