Graph data structures effectively represent objects and their relationships, enabling the modeling of complex connections in various fields. Recent work demonstrate that metal at diagonal crossbar arrays (m-CBA) can effectively represent planar graphs. However, they are unsuitable for representing multilayer graphs having multiple relationships across different layers. Using conventional software, embedding multilayer graphs in high-dimensional Euclidean spaces introduces significant mathematical complexity and computational burden, often resulting in information loss. This study proposes a unique graph embedding (mapping) method utilizing a fabricated vertical m-CBA (vm-CBA), where a custom-built measurement system thoroughly validated its functionality. This structure directly maps multilayer graphs into a 3D vm-CBA, accurately representing inter-layer and intra-layer connections. The practical link prediction and information scores across various real-world datasets demonstrated that vm-CBA achieved enhanced accuracy compared to conventional embeddings, even with a significantly decreased number of operations.