Severe acute respiratory syndrome (SARS) first appeared in 2002 in China, which fastly affected about 8000 patients over 29 countries and caused 774 fatalities. As its pathogen was identified as a new kind of coronavirus (SARS_CoV), its genome was quickly sequenced on several isolates. Studies on its functional genomics were performed by combinatorial application of all the available bioinformatics tools and the development of new programs. In this way, it was found that the four proteins were absolutely responsible for nosogenesis of SARS, i.e. spike (S) protein; small envelop (E) protein; membrane (M) protein; and nucleocaspid (N) protein. Molecular evolution studies have revealed that SARS must be originated from wild animals, and it was demonstrated that the major genetic variations in some critical genes, particularly the Spike gene, was essential for the transition from animal-to-human transmission to human-to-human transmission. Theoretical models, either Logistic model or SIR model, were developed to describe the transmission of SARS. The recorded difference of SARS spreading in Beijing and Hong Kong was also reasonably analyzed according to these models. The whole process of fruitful bioinformatics studies, along with other related scientific investigations have set up an unprecedented paradigm for human of how to battle against sudden-breaking and catastrophic epidemics.