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Since integrated circuits are performed by several untrusted manufacturers, malicious circuits (hardware Trojans) can be implanted in any stage of the Internet-of-Things (IoT) devices. With the globalization of the IoT device manufacturing technologies, protecting the system-on-chip (SoC) security is always the keys issue for scientists and IC manufacturers. The existing SoC high-level synthesis approaches cannot guarantee both register-transfer-level and gate-level security, such as some formal verification and circuit characteristic analysis technologies. Based on the structural characteristics of hardware Trojans, we propose a multi-layer hardware Trojan protection framework for the Internet-of-Things perception layer called RG-Secure, which combines the third-party intellectual property trusted design strategy with the scan-chain netlist feature analysis technology. Especially at the gate level of chip design, our RG-Secure is equipped with a distributed, lightweight gradient lifting algorithm called lightGBM. The algorithm can quickly process high-dimensional circuit feature information and effectively improve the detection efficiency of hardware Trojans. In the meanwhile, a common evaluation index F-measure is used to prove the effectiveness of our method. The experiments show that RG-Secure framework can simultaneously detect register-transfer-level and gate-level hardware Trojans. For the trust-HUB benchmarks, the optimized lightGBM classifier achieves up to 100% true positive rate and 94% true negative rate; furthermore, it achieves 99.8% average F-measure and 99% accuracy, which shows a promising approach to ensure security during the design stage.