Secure communication is a promising technology for wireless networks because it ensures secure transmission of information. In this paper, we investigate the joint subcarrier (SC) assignment and power allocation problem for non-orthogonal multiple access (NOMA) amplify-and-forward two-way relay wireless networks, in the presence of eavesdroppers. By exploiting cooperative jamming (CJ) to enhance the security of the communication link, we aim to maximize the achievable secrecy energy efficiency by jointly designing the SC assignment, user pair scheduling and power allocation. Assuming the perfect knowledge of the channel state information (CSI) at the relay station, we propose a low-complexity subcarrier assignment scheme (SCAS-1), which is equivalent to many-to-many matching games, and then SCAS-2 is formulated as a secrecy energy efficiency maximization problem. The secure power allocation problem is modeled as a convex geometric programming problem, and then solved by interior point methods. Simulation results demonstrate that the effectiveness of the proposed SSPA algorithms under scenarios of using and not using CJ, respectively.