Knowledge graphs (KGs) are becoming essential resources for many downstream applications. However, their incompleteness may limit their potential. Thus, continuous curation is needed to mitigate this problem. One of the strategies to address this problem is KG alignment, i.e., forming a more complete KG by merging two or more KGs. This paper proposes i-Align, an interpretable KG alignment model. Unlike the existing KG alignment models, i-Align provides an explanation for each alignment prediction while maintaining high alignment performance. Experts can use the explanation to check the correctness of the alignment prediction. Thus, the high quality of a KG can be maintained during the curation process (e.g., the merging process of two KGs). To this end, a novel Transformer-based Graph Encoder (Trans-GE) is proposed as a key component of i-Align for aggregating information from entities’ neighbors (structures). Trans-GE uses Edge-gated Attention that combines the adjacency matrix and the self-attention matrix to learn a gating mechanism to control the information aggregation from the neighboring entities. It also uses historical embeddings, allowing Trans-GE to be trained over mini-batches, or smaller sub-graphs, to address the scalability issue when encoding a large KG. Another component of i-Align is a Transformer encoder for aggregating entitie’ attributes. This way, i-Align can generate explanations in the form of a set of the most influential attributes/neighbors based on attention weights. Extensive experiments are conducted to show the power of i-Align. The experiments include several aspects, such as the model’s effectiveness for aligning KGs, the quality of the generated explanations, and its practicality for aligning large KGs. The results show the effectiveness of i-Align in these aspects.