This study investigates the physical layer secrecy of a backscatter communication (BC)-based multi-user time division multiple access (TDMA) mobile edge computing (MEC) Internet of Things (IoT) system. Specifically, an unmanned aerial vehicle (UAV) equipped with a server hovers over an energy-constrained mobile IoT device cluster to transfer RF energy and assist them in executing their tasks by employing the backscatter communication scheme. To enhance the secrecy of the considered system, a partial offloading scheme is proposed based on the non-linear harvested energy levels of users. Accordingly, a closed-form expression for the secrecy successful computation probability (SSCP) is derived, which jointly considers the harvested energy for local computing, offloading and processing latency, as well as secrecy capacity. The impact of key parameters on secrecy and latency performance is investigated to reveal the system’s behavior. Numerical results from computer simulations are provided to verify the correctness of our analysis.