The acupuncture point mapped into the body meridian line has been the subject of extensive research / however, the scientific basis of the body meridian line remains unknown. In the present study, a pair of line-magnets was attached along the heart meridian line between HT4 and HT6 (intervention), and heart rate variability (HRV) was examined in a double-blind, randomized, crossover trial. Forty-five healthy young adults were randomly assigned into two groups and received two interventions in a different order. The only difference between the interventions was that the magnet pole was swapped. The results showed that the frequency-domain (LF, LF/HF) properties of HRV, which reflects underlying autonomic nervous system activity, changed when the magnetic pole’s direction along the heart meridian line was changed. This finding suggests that a line-magnet attached along to the heart meridian line may affect the cardiovascular system.