LLM-based agents are rapidly being deployed in real-world applications (e.g., digital assistants and customer service), making safety a critical concern. However, in multi-turn, tool-augmented settings, dynamic user interactions, external tool use, and unintended harmful behaviors make robust safety assurance challenging. To address these challenges, we propose **SafeAgent**, a framework that improves agent safety through fully automated synthetic data generation. SafeAgent introduces (1) an open and extensible threat model OTS that decomposes agent risk into instruction-, context-, and action-induced sources to ground safety analysis and alignment; and (2) an automated pipeline that instantiates OTS to surface scenario-specific failure modes, stress-test agents, and generate self-reflective safe responses—without hazardous real-world data collection. We evaluate SafeAgent on two safety benchmarks and one real-world terminal task. Across four widely used open-source models, SafeAgent improves safety performance by 45% on average and delivers a 28.91% gain on the real-world task, outperforming state-of-the-art closed-source models. These results highlight the practical advancement and scalability of SafeAgent in building safer LLM agents for real-world deployment.