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IEEE 802.15.4 protocol defines multiple security specifications to provide different levels of safety protection in the link layer. How to choose the security level for harvesting enabled Internet of Things (IoT) nodes is an important problem as it decides the security protection and also impacts on network performance. Considering the dynamics of network threats and harvesting performance, in this letter, a harvesting and threat aware security configuration strategy is proposed. Simulation results illustrate that the proposal can choose the suitable security configuration according to the network security threats, service requirements, and the variable harvested energy. Comparison with conventional methods, the proposed strategy can extend the working time, resulting in improved network performance. Moreover, the proposed security configuration method can also meet the diversified service requirements.