The traditional link layer security mechanism can not fundamentally protect the security of information transmission of wireless communication system. In order to solve the problem, a parallel interpolation encryption algorithm based on the parallel modulation characteristics of Orthogonal Frequency Division Multiplexing (OFDM) system and physical layer security was proposed. Firstly, the number of inserted symbols was determined by the number of subcarriers modulated by the OFDM system, and the positions of inserted symbols were generated under the control of key. Secondly, the original OFDM symbols before and after the position of inserted symbol were taken out, and the inserted symbol was determined by calculating the mean value of these symbols. Finally, the pseudo-random interpolation was completed after Inverse Fast Fourier Transform (IFFT). Compared with the traditional link layer security methods, the proposed algorithm can realize the whole encryption of modulation symbols, ensure the security of signaling, flag and data information, and reduce the complexity of algorithm effectively. The simulation experimental results show that, the proposed algorithm can effectively resist a variety of eavesdropping attacks and has little influence on the inherent performance of communication system. Furthermore, the proposed algorithm can be well adapted to Gaussian channel and multipath channel, and shows a certain ability to resist multipath fading.