Abstract: New beam line was constructed on the 2×3 MV tandem accelerator in the Institute of Modern Physics, Fudan University, for the development of a biological single-ion microbeam. Accelerated ion beam will first be deflected by 30° by an analyzing magnet and bended vertically up by 90° to the end of the beam line. Borosilicate glass capillary, with the inner diameter of 1.5 μm, was installed at the end of the beamline to extract an ion microbeam. A special structure of scintillator film and photomultiplier installed at the endstation of the microbeam exit was used for precise detection and counting of the microbeam ions. A high voltage beam deflector was installed on the beam line for a fast beam cutting action when pre-defined number of microbeam ions had arrived to target cells. Based on the overall design, low energy proton microbeam, with the energy of 3 MeV, FWHM<60 keV and a spatial resolution within 2.2 μm has been acquired in current experiment. Quantitative irradiation by the collimated microbeam has shown a precision above 95%. In this paper, the basic design and development progress of the microbeam facility was introduced, including the relevant parts of beamline design, microbeam generation, high voltage beam deflector and single-ion detection.