LLM-based autonomous agents possess capabilities such as reasoning, tool invocation, and environment interaction, enabling the execution of complex multi-step tasks. The internal reasoning process, i.e., thought, of behavioral trajectory significantly influences tool usage and subsequent actions but can introduce potential risks. Even minor deviations in the agent's thought may trigger cascading effects leading to irreversible safety incidents. To address the safety alignment challenges in long-horizon behavioral trajectories, we propose Thought-Aligner, a plug-in dynamic thought correction module. Utilizing a lightweight and resource-efficient model, Thought-Aligner corrects each high-risk thought on the fly before each action execution. The corrected thought is then reintroduced to the agent, ensuring safer subsequent decisions and tool interactions. Importantly, Thought-Aligner modifies only the reasoning phase without altering the underlying agent framework, making it easy to deploy and widely applicable to various agent frameworks. To train the Thought-Aligner model, we construct an instruction dataset across ten representative scenarios and simulate ReAct execution trajectories, generating 5,000 diverse instructions and more than 11,400 safe and unsafe thought pairs. The model is fine-tuned using contrastive learning techniques. Experiments across three agent safety benchmarks involving 12 different LLMs demonstrate that Thought-Aligner raises agent behavioral safety from approximately 50% in the unprotected setting to 90% on average. Additionally, Thought-Aligner maintains response latency below 100ms with minimal resource usage, demonstrating its capability for efficient deployment, broad applicability, and timely responsiveness. This method thus provides a practical dynamic safety solution for the LLM-based agents.