The invention relates to a heavy ion micro beam positioning method and a chip used in the method, and belongs to the technical field of heavy ion micro beam irradiation. A positioning test circuit which includes at least one pair of vertical edges and one pair of horizontal edges is set in the chip, the internal of the edges of the positioning test circuit serves as sensitive areas, and a heavy ion micro beam input to the sensitive area can generate a single-particle transient pulse signal. The method comprises that an amplification device determines a position of the positioning test circuit; the positioning test circuit is positioned near a beam spot of the heavy ion micro beam; the vertical and horizontal edges of the positioning test circuit pass the beam spot; the pulse numbers and position images in the directions of axes X and Y are obtained; and a coordinate (X0, Y0) is obtained, and a coordinate (X0+deltaX, and Y0+deltaY) of another to-be-detected position on the chip is obtained according to the position (deltaX, deltaY) of the to-be-detected position relative to the position of the positioning test circuit. The method has the advantages that both positioning steps and errors are reduced, and the other to-be-detected positions can be positioned rapidly and accurately.