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In this paper, we investigate the energy-efficient secure uplink transmission for the wireless powered Internet of Things (IoT), where one energy-constrained source and multiple energy-constrained relays harvest energy from multiple power beacons (PBs) in the presence of a passive eavesdropper. To perform energy-efficient secure communications, we consider three relay selection schemes with the best PB selected by the source, i.e., the best relay is selected randomly, the best relay is selected by the source, and the best relay is selected by the best PB (BRBP), respectively. For each scheme, the exact closed-form expressions of power outage probability (POP), secrecy outage probability (SOP), and secure energy efficiency (SEE) are derived over the Rayleigh fading channel. Furthermore, we formulate the SEE maximization problem under the transmit power constraint to optimize the transmit power in PBs and the time-switching factor. Considering the resource limitation for IoT devices, we adopt a low-complexity Dinkelbach algorithm combined with Brent's method to solve this multi-parameter fractional optimization problem. Simulation results demonstrate that the BRBP scheme achieves the best SOP performance and either increasing the number of PBs or decreasing the threshold of POP can significantly improve the SEE of the considered system.