Functional magnetic resonance imaging (fMRI) has been widely used in the research of acupuncture mechanism in recent years. This article analyzes the effect of four main influencing factors, i.e., research subject, selection of acupoints, manipulation of acupuncture and evaluation of Deqi, and examples are given to explain research application of these four aspects. Based on those mentioned above, the authors presumed that removing ex terior and interior factors of research subject, optimizing compatibility of acupoints and manipulations of acupuncture and making use of correct evaluation scale of Deqi can improve the scientificity and objectivity of fMRI for evaluation of acupuncture mechanism research.