We have investigated the changes of electroencephalography (EEG) and electrocardiography (ECG) under pulsed magnetic field (PMF) and acupuncture stimulus on acupoint PC9. In order to compare quantitatively the effect of PMF and acupuncture stimulus, the difference of alpha activities are calculated from EEG spectra, and the spectrum curves of ECG were analyzed in the frequency domain of heart rate variability (HRV). The increase of alpha activities after both stimuli could be explained that the impulse of stimulus on PC9 might pass through sensory nerve following meridian and approach the cerebral cortex, causing the central nervous system (CNS) to be activated for pacifying emotion and calming the mind. The decrease in sympathovagal activity of HRV after both stimuli indicates that parasympathetic nerves were activated and the sympathetic nerves were in constrained condition. These findings suggest that PMF could be patient-friendly alternative non-invasive medical treatment for influencing human physiology, in comparison with acupuncture inserting the needle and inducing nervous and anxious state to subject.