Abstract: The material utilization and uniformity of isotopic target prepared by focused heavy ion beam sputtering were studied. The longitudinal and transverse thickness distributions were determined for two sputtering distances (7 mm and 14 mm). The effective means of improving the uniformity, such as substrates revolution and reversing for the half thickness were obtained by experimental measurement. The optimum geometric parameters for matching material utilization and uniformity were got. Five isotopic oxide targets and nine high-melting-point metal isotopic targets applied to the experiment of nuclear physics were prepared by focused heavy ion beam sputtering. For the source-substrate distances of 7 mm and 14 mm and an area of 9 mm×10 mm on a target, the experiment results indicate that the maximum material utilization and uniformity can be obtained if the vertical distances between the substrate center and the target area are 9 mm and 11 mm, respectively.