By the in-depth excavation of prescriptions containing herbal pair Acori Tatarinowii Rhizoma-Polygalae Radix in the Dictionary of Traditional Chinese Medicine Prescriptions, this study analyzed their formulation rules, so as to provide reference for their clinical application and new drug development. First, the prescriptions containing Acori Tatarinowii Rhizoma-Polygalae Radix were collected from the Dictionary of Traditional Chinese Medicine Prescriptions, and their indications, herbal compatibility, and dosage forms were analyzed statistically using the Traditional Chinese Medicine Inheritance Support System(TCMISS). Meanwhile, the formulation rules and common dosage forms for the top four indications(amnesia, palpitation, mania, and epilepsy) sorted by frequency were analyzed with Apriori algorithm. A total of 507 prescriptions containing Acori Tatarinowii Rhizoma-Polygalae Radix were screened out, involving 15 indications(frequency>10) like amnesia, palpitation, mania, and epilepsy. There were 30 commonly used Chinese herbs(frequency≥60), with the Qi-tonifying herbs(Ginseng Radix et Rhizoma and Glycyrrhizae Radix et Rhizome), mind-tranquilizing herbs(Poria and Poria cum Radix Pini), and Yin-nourishing herbs(Angelicae Sinensis Radix and Ophiopogonis Radix) being the core ones. The commonly used dosage forms were honey pill, paste pill, decoction, and powder. These have indicated that the herbal pair Acori Tatarinowii Rhizoma-Polygalae Radix is often combined with Qi-tonifying, Yin-nourishing, and mind-tranquilizing herbs for the treatment of "heart or brain diseases" caused by phlegm production due to spleen deficiency, Qi and blood deficiency, and phlegm-turbidity blocking orifice. In the treatment of amnesia, supplementing essence and replenishing marrow are considered on the basis of tonifying Qi, nourishing Yin, and tranquilizing mind. In the treatment of palpitation and mania, tranquilizing mind is emphasized. In the treatment of epilepsy, the emphasis is placed on resolving phlegm, extinguishing wind, and stopping convulsion.