Abstract: As a key technology to study the physical mechanism of single event effects (SEEs) and to identify the sensitive area of microelectronic devices, heavy ion micro-beam irradiation has been paid more and more attention by researchers. Single ion hit (SIH) is an important part of heavy ion micro-beam irradiation, which could reduce the number of incident ions to just one through a series of monitoring and control methods. Owing to this background, the single ion hit (SIH) system was established based on the pinhole heavy ion micro-beam facility in Beijing HI-13 tandem accelerator. To realize single ion hit, it is necessary to cut off the beam current immediately after monitoring the first ion incidence, so as to avoid the next ion passing through the beam switch. Therefore, the beam monitoring device is important to SIH system. The beam monitoring device consists of a 7 nm carbon film, a secondary electron detector and a beam monitoring computer. There is a fixed coefficient K between the number of ions incident on the device and the number of secondary electrons collected by the secondary electron detector. According to the value of K, the number of incident ions can be controlled by the number of secondary electrons. Through the analysis of the potential factors affecting the SIH performance, the theoretical reference formula of factors that affect the accuracy of SIH was given. The three main factors, K, beam intensity and shutter time were experimentally. The results show that the accuracy of this SIH system can reach 90% when the shutter time is 60 ms and the beam intensity is low. At the same time, lower beam intensity and shorter shutter tim are conducive to continuously improving the SIH performance. However, due to the technology limitation of the accelerator, the intensity and uniformity of the beam cannot be achieved at the same time. If the current intensity is too low, the uniformity will become much worse. Therefore, the single ion hit experiment should be carried out when the beam is relatively uniform and the K is stable. At last, the SIH system was applied to 28 nm SRAM device irradiation to reduce the interference of multiple ion incidence. Different patterns and the distribution of multiple cell upsets (MCUs) induced by the single ion were obtained, which verified the availability of the system in the research of radiation effect mechanism of nano devices. Based on the SIH system, it can be determined that all the MCUs are real events without obtaining chip layout information or post processing of data, which could improve data analysis efficiency and provide more real-time information for the experimental personnel.