The collaborations of the diseases might be the key to understand the mechanism of the diseases since it is difficult to detect the role of complex genes and micro RNA in diseases. With the rapid development of technology, several metabolites of many kinds of diseases could be obtained by the advanced machines. Some diseases are related to several metabolites, and some metabolites have strong relationship with several diseases. Since there is certain relationship between different diseases, firstly we should find the similarity of different diseases. Then the similarity of different metabolites could be calculated by the relationship of diseases. Then a network of metabolites' similarity could be built. After building up the network, the diseases might not only relate to originally several metabolites, but more related metabolites to the disease could be found by the lines of the network. It can be used to explain the mechanism of the diseases more precisely. These metabolites could also be candidates to map the diseases in terms of the similarities. We can also sort these potentially relevant metabolites by similarity. It offers researchers a novel way to find out metabolites which is related to diseases.