The invention discloses a clinical decision support system and method based on workflows. The clinical decision support system comprises a calling client-side, a medical examination instrument client-side, a workflow modeling tool module, a workflow engine module, a rule engine module, an inference engine module, a file storage server, a clinical pathway model case base and a diagnosis rule base. Through a distributed network, computers, servers, X-ray machines, electrocardiographs and other examination instruments in a hospital are connected, and being combined with standard clinical pathways issued by state authorized hospitals, the clinical decision support system achieves the intelligence orienting any disease field through multi-client-side cooperation. According to the clinical decision support method based on the workflows, a medical clinical path definition, a workflow modeling tool, a dispatching function of a workflow engine and a file managing function of a storage server are utilized reasonably, standard diagnosis and treat procedures can be customized according to any diseases by combining clinical paths, and the method can provide decision support for users at two critical decision points of primary diagnosis and final definite diagnosis.