In this paper, we consider both energy efficiency and security issues in a wireless power transfer (WPT) enabled relay system. In the considered system, the multiple-antenna decode-and-forward relay node (RN) has both information decoding and wireless power recycling capabilities, and thus can be empowered by WPT and assist the transmission from the multiple-antenna base station (BS) to the mobile terminals (MTs). In addition, we consider that there is an eavesdropper between the BS and the RNs, which tries to overhear the information sent to the MTs. We formulate a joint optimization problem with the objective to optimize energy efficiency of the presented system by considering WPT time allocation, power allocation, and secrecy data rate. In particular, we propose to select RNs based on different assigned priorities so that the physical layer security of information transmission can be guaranteed. Moreover, we take into consideration of the cases that the RNs adopt the half- and full-duplex protocols, and study the corresponding system performance analytically. The proposed schemes are evaluated by extensive simulations and it is demonstrated that the proposed resource allocation schemes can obtain energy efficiency maximization, and have superior performance over other schemes.