The invention discloses a physical layer watermark authentication method and system for an LTE system, and belongs to the field of physical layer watermark authentication. A physical layer authentication technology is applied to an LTE system, system overhead required by traditional high-level authentication is reduced, and a traditional watermark authentication scheme is improved as follows: a watermark is embedded into a phase of a reference signal, interference of the watermark to a user signal is reduced, and meanwhile, by adopting a phase symmetric embedding mode, the influence of the watermark on the channel estimation of the reference signal is reduced; according to the method, the concept of pseudo user bits is provided, the pseudo user bits are used for replacing user bits to serve as parameters for watermark generation, and authentication errors caused by user signal demodulation errors of a receiving end are reduced; in addition, channel codes are added into a watermark generation scheme, and error codes generated in the watermark transmission process are reduced.