Despite the strong performance of Transformers, their quadratic computation complexity presents challenges in applying them to vision tasks. Automatic pruning is one of effective methods for reducing computation complexity without heuristic approaches. However, directly applying it to multi-head attention is not straightforward due to channel misalignment. In this paper, we propose an automatic channel pruning method to take into account the multi-head attention mechanism. First, we incorporate channel similarity-based weights into the pruning indicator to preserve more informative channels in each head. Then, we adjust pruning indicator to enforce removal of channels in equal proportions across all heads, preventing the channel misalignment. We also add a reweight module to compensate for information loss resulting from channel removal, and an effective initialization step for pruning indicator based on difference of attention between original structure and each channel. Our proposed method can be used to not only original attention, but also linear attention, which is more efficient as linear complexity with respect to the number of tokens. On ImageNet-1K, applying our pruning method to the FLattenTransformer, which includes both attention mechanisms, shows outperformed accuracy for several MACs compared with previous state-of-the-art efficient models and pruned methods. Code will be available soon.