The invention discloses multifunctional intelligent acupuncture and moxibustion diagnosis and treatment instrument and an application method thereof. The diagnosis and treatment instrument comprises an acupuncture point detection module, an acupuncture point positioning module and an acupuncture and moxibustion therapy module which can be used separately or as a whole, wherein the acupuncture point detection module is used for collecting information of body surface impedance, acoustic electricity, infrared temperature, luminescence intensity, biomagnetism and electromyogram; the acupuncture point positioning module is used for lively and directly displaying the acupuncture point positions on a human 3D (three-dimensional) model, and conducting objective and accurate positioning by combining position relation of human skeleton, muscle, vessel, nerve, lymph or viscera and acupuncture points, without influence by body figure difference of users; and the acupuncture and moxibustion therapy module is used for realizing multiple treatment of oscillation massaging, infrared thermal therapy, electromagnetic treatment, pulse current treatment and the like. The multifunctional intelligent acupuncture and moxibustion diagnosis and treatment instrument and the application method thereof have the advantages of precisely detecting all physical characteristics of the acupuncture points, providing complete and reliable diagnosis reference and basis for patients and medical staff, providing accurate and reliable positioning results, and adopting multiple acupuncture and moxibustion therapymeans so as to provide convenience to users.