This paper studies the physical layer security of uplink (UL) transmission in simultaneous wireless information and power transfer (SWIPT) deployed in wireless sensor networks (WSNs). Firstly, we model the random network as Poisson cluster process (PCP) to focus on the case where eavesdroppers hide around certain targets to intercept the confidential information successfully. Then, the communication model of time division multiple access (TDMA) is established to avoid inter-node interferences and extend the time for energy harvesting (EH). After that, aiming at the sensor nodes that work in “harvesting-transmitting” (H-T) mode with time switching (TS) receiver, we derive the energy outage probabilities (EOP), connection outage probabilities (COP) and secrecy outage probabilities (SOP) through comprehensive analysis on downlink (DL) and UL transmissions, based on which the uplink secrecy throughput (STP) is obtained to characterize the overall performance. Finally, our theoretical derivations are verified and the influences of various parameters on uplink STP are revealed by the simulation results, which indicate the existence of an optimal energy threshold and a partition coefficient of DL and UL period that can achieve the best secrecy performance.