In metabolomics, metabolic pathway is represented by well-displayed graph. Metabolic pathways, especially, have a complex binding structure, which makes the graphical representation hard to visualize. There is a problem that edge crossings exponentially increase as the number of nodes grows. To apply automatic graph layout techniques to the genome-scale metabolic flow of metabolism domains, it is very important to reduce unnecessary edge crossing on a metabolic pathway layout. we proposed a metabolic pathway layout algorithm based on 2-layer layout. Our algorithm searches any meaningful component existing in a pathway, such as circular components, highly connected nodes, and the components are drawn in upper layer. Then the remaining subgraphs except meaningful components are drawn in lower layer by utilizing a new radial layout algorithm. It reduces ultimately reduced the number of edge crossings. This algorithm is the basis of flexible analysis for metabolic pathways.