As one of the main candidates for future civil aviation communications systems, the L-band digital aeronautical communication system (L-DACS) is expected to achieve secure and reliable transmission. Due to the broadcasting nature of air–ground wireless links, the L-DACS has the risk of being intercepted by malicious eavesdroppers, which negatively affects aviation communication security. In addition, because the spectrum of the L-DACS overlaps with the aviation distance measuring equipment (DME), the pulse interference caused by the DME signal may lead to the wireless link being more fragile and susceptible to wiretapping. In this paper, with a focus on enhancing wireless transmission security, we propose a comprehensive physical layer security (PLS) method for the L-DACS. The key to the proposed PLS method is restraining the transmission of the eavesdropper by injecting artificial noise into the transmitted signal while improving the transmission of the legitimate receiver through the adoption of pulse interference mitigation. First, to characterize the L-DACS in the secure scene, we derive the signal-to-interference-plus-noise ratio (SINR) of the legitimate receiver and any potential eavesdropper by constructing equivalent noise. Next, from the perspective of the information theory, we derive the closed form of the secrecy capacity of the L-DACS by employing the proposed PLS methods with three kinds of nonlinear interference mitigation: including ideal pulse blanking, peak threshold-based pulse blanking, and peak threshold-based pulse clipping. Finally, we compare and analyze different ways to enhance the secrecy capacity of the proposed PLS method using various interference mitigation methods.