Provided are a method and system for allocating wavelength channels in a Passive Optical Network (PON), and an Optical Line Terminal (OLT). In the method, an OLT may acquire pre-set wavelength channel priority information and Optical Network Unit (ONU) priority information; and the wavelength channel priority information and the ONU priority information may be sent to each ONU to enable each ONU to selectively access a corresponding wavelength channel according to the wavelength channel priority information and the ONU priority information based on a pre-set rule.