The identification and secure transmission of the station phase codes in the Loran C system are the premise of judging chains and receiving signals for hyperbolic positioning. Aiming at the problem that the Loran C system cannot achieve high security transmission by classical means, we propose a phase code transmission scheme based on EPR state quantum signals and analyse the security of this scheme under the entanglement attack and spectroscopic attack. The relationship between the information transmission efficiency and the transmission coefficient of the spectroscope as well as that between the information transmission efficiency and the compression degree of the spectroscope is obtained, which verifies that the proposed scheme can effectively improve the security of phase code transmission between the main station and the secondary station in the Loran C system.