In order to explore the potential therapeutic effect of Xanthoceras sorbifolia Bunge. against Alzheimer’s disease, an HPLC-MS/MS method has been developed and validated for simultaneous determination in rat brain of eight neurotransmitters, including dopamine, norepinephrine, 5-hydroxy-tryptamine, acetylcholine, l-tryptophan, γ-aminobutyric acid, glutamic acid and aspartic acid with a simple protein precipitation method for sample pre-treatment. The brain samples were separated on a polar functional group embedded column, then detected on a 4000 QTrap HPLC-MS/MS system equipped with a turbo ion spray source in positive ion and multiple reaction monitoring mode. The method was fully validated to be precise and accurate within the linearity range of the assay, and successfully applied to compare the neurotransmitters in the rat brain from four groups of normal, Alzheimer’s disease, and the oral administration group of X. sorbifolia extract and huperzine. The results indicated that brain levels of dopamine, norepinephrine and acetyl choline all decreased in the AD rats, while l-tryptophan showed an opposite trend. After administration of the Xanthoceras sorbifolia extract and huperzine, the level of acetyl choline and tryptophan returned to normal. Combination of the metabolic analysis, the results indicated that acetyl choline and l-tryptophan could be employed as therapy biomarkers for AD, and the results shown that the crude extract of the husks from Xanthoceras sorbifolia might ameliorate the impairment of learning and memory in the Alzheimer’s disease animal model with similar function of AchEI as huperzine. The established method would provide an innovative and effective way for the discovery of novel drug against Alzheimer’s disease, and stimulate a theoretical basis for the design and development of new drugs.