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.