SynBioChem: With the rapid development of computer technology, big data has become a boom in society, which can not only be used in the field of politics, economy and military affairs, but also be applied in life science research field. For the past few years, synthetic biology has played an important role in producing biofuels,bulk chemicals and natural products, thus making many products realize the industrialization. This research integrates the knowledge of computer, biology, chemistry and mathematics. From more than two hundred thousand references in PubMed related to synthetic biology, we extract all kinds of valuable information about small molecular compound, including the name, synonyms, structure, reactions and some other reference information, finally leading to the construction of small molecular compound database based on synthetic biology. This database has the advantages of accurate data, comprehensive information and good compatibility system, which is certainly helpful to produce new drugs and energy using the way of synthetic biology and promote sustainable development of human society greatly.