By incorporating visual inputs, Multimodal Large Language Models (MLLMs) extend LLMs to support visual reasoning. However, this integration also introduces new vulnerabilities, making MLLMs susceptible to multimodal jailbreak attacks and hindering their safe deployment.Existing defense methods, including Image-to-Text Translation, Safe Prompting, and Multimodal Safety Tuning, attempt to address this by aligning multimodal inputs with LLMs' built-in safeguards.Yet, they fall short in uncovering root causes of multimodal vulnerabilities, particularly how harmful multimodal tokens trigger jailbreak in MLLMs? Consequently, they remain vulnerable to text-driven multimodal jailbreaks, often exhibiting overdefensive behaviors and imposing heavy training overhead.To bridge this gap, we present an comprehensive analysis of where, how and which harmful multimodal tokens bypass safeguards in MLLMs. Surprisingly, we find that less than 1% tokens in early-middle layers are responsible for inducing unsafe behaviors, highlighting the potential of precisely removing a small subset of harmful tokens, without requiring safety tuning, can still effectively improve safety against jailbreaks. Motivated by this, we propose Safe Prune-then-Restore (SafePTR), an training-free defense framework that selectively prunes harmful tokens at vulnerable layers while restoring benign features at subsequent layers.Without incurring additional computational overhead, SafePTR significantly enhances the safety of MLLMs while preserving efficiency. Extensive evaluations across three MLLMs and five benchmarks demonstrate SafePTR's state-of-the-art performance in mitigating jailbreak risks without compromising utility.