Synergetic effects occur when the efficacy of herbs are combined. The scientific interpretation of these properties is a benefit to the explanation of the compatibility rule and it is further beneficial to the action mechanism of formulae. Synergy refers to the efficacy of combinations of herbs that is greater than the summed responses of each individual herb. As shown in Figure 3, Salvia miltiorrhiza, Panax notoginseng, Dalbergia odorifera, and Astragalus membranaceus all participate in the energy metabolism process, including cAMP metabolic process, carbohydrate metabolic process, and lipid metabolic process, and they hence have the synergetic effect on enhancing the Qi efficacy of QSYQ. The regulation of blood coagulation is involved by four herbs which reinforce the efficacy of promoting the blood circulation of QSYQ. This indicated that the synergy of formula can be illustrated based on the functional modules.