Sparse autoencoders (SAEs) are widely used to interpret the internal representations of large language models (LLMs), yet their reliability under post-hoc model compression remains poorly understood. We present a systematic study of how pruning affects SAE behavior and theoretically show that, for a fixed SAE, its impact is governed by perturbation energy, a covariance-weighted norm. This perspective exposes a key limitation of magnitude pruning: by ignoring activation geometry, it distorts the learned representation space and degrades SAE functionality. Activation-aware methods such as Wanda and SparseGPT, in contrast, implicitly control perturbation energy and are therefore substantially more robust at preserving SAE behavior. We further reveal a consistent structural vulnerability across all pruning methods: middle layers are significantly more sensitive to pruning than early or late layers. Guided by this insight, we propose a layer-wise sparsity allocation strategy, achieving lower perplexity under the same average pruning sparsity. Experiments across four model architectures validate our theoretical findings. Code is publicly available at https://github.com/osu-srml/sae-robustness-under-pruning/tree/main.

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