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A new detection method has been applied to study the penetration depth of low-energyheavy ions in botanic samples. Highly oriented pyrolytic graphite (HOPG) pieces were placed behind the target samples with certain thickness to receive energetic penetrated ions during the irradiation. After irradiation, statistic number density of protrusion-like damage induced by energetic penetrated ions can be obtained through scanning tunneling microscope (STM) observation on the surfaces of HOPG. The results of test indicate that the detection limit can be as low as 1.0× 109protrusions/em2. With the method, the penetration depth of at least 60μm can be detected in kidney bean slices irradiated by N+ ions with dose of 0.3-3× 1017ions/cm2.