Through our pre-investigation and literature analysis, it was found that rhubarb could be categorized into two types, chrysophanol-type and rhein-type, based on the proportion of the two constituents in the total content of anthraquinones after acid hydrolysis. In this paper, the antimicrobial activities of chrysophanol-type and rhein-type rhubarbs against Staphylococcus aureus were compared with microcalorimetric analysis, in order to illustrate the bioactive differentiability between the two chemotypes. For the aim to display the distinction of chrysophanol and rhein percentage in total anthraquinones, the sampling volume was regulated to make the total anthraquinones equivalent, thus, the antimicrobial difference was only attributed to the difference of chemotypes. The results indicated that the antimicrobial difference between the two chemotypes was confirmable labeled at the biothermokinetic parameters of S. aureus growth affected by the rhubarb samples. The growth rate constant (k1) of the first exponential phase for the growth of S. aureus affected by the rhein-type rhubarb was significantly lower than that of chrysophanol-type (P<0.01), which suggested stronger antimicrobial activity of rhein-type rhubarb than that of chrysophanol-type. However, the antimicrobial activities of rhein-type rhubarbs were not positively correlated to the contents of rhein. It suggested that the antimicrobial activity of rhubarb might be related to some unknown components which were of same accumulating pattern of rhein. The findings in present study provided some experimental evidence on categorizing rhubarb into two chemotypes through the difference of antimicrobial activity on S. aureus by microcalorimetric analysis and, further, offered references to revision of the commercial specification of rhubarb from chemical view.