Alzheimer's disease (AD) is an age-related neurodegenerative disease, affecting over 20 million people worldwide. Until recently, two major hypotheses were proposed regarding the molecular mechanism of pathogenesis: the cholinergic hypothesis and the amyloid cascade hypothesis. At present, acetylcholinesterase inhibitors are the most effective therapy for AD. Most pharmacological research has focused on the ability of acetylcholinesterase to alleviate cholinergic deficit and improve neurotransmission. Coptidis rhizoma and its isolated alkaloids are reported to possess a variety of activities, including neuroprotective and antioxidant effects. However, as yet no theoretical analysis exists to support this hypothesis. To examine this theory, we applied a computational pharmaceutical analysis to reveal that Chinese medicine Coptidis rhizoma alkaloids have much higher activities than Donepezil (commercial name is Aricept) by docking and scoring.