Disclosed are a physical layer steganographic transmission method and system, wherein same are applied to the technical field of communications. In the method of the present embodiment, when a steganographic signal is transmitted each time, an upper limit of a steganographic capacity is determined after a signal sending end performs channel coding on a carrier signal, and a random sequence is generated for indicating an embedding position of a first hidden signal in the coded carrier signal; then, the first hidden signal is embedded into the carrier signal according to the generated sequence so as to obtain the steganographic signal, wherein the length of the first hidden signal cannot be greater than the upper limit of the steganographic capacity; and finally, the sending end sets a transmission identifier in the steganographic signal and modulates same and sends same out. Thus, in the present embodiment, a sending end dynamically and self-adaptively adjusts the maximal length of a first hidden signal embedded into a carrier signal each time, and a second hidden signal with a relatively long length needing to be transmitted can be transmitted multiple times, so that a steganographic signal cannot be easily suspected by an adverse monitoring end, and thus, the security of hidden signal transmission is improved.