The invention relates to an automatic ICSI system capable of accurately identifying, which comprises a power supply module, a main control module, a sample optical observation module, a user interaction module, a sperm capturing unit, an ovum fixing unit and a single sperm injection unit, the sample optical observation module, the user interaction module, the sperm capturing unit, the ovum fixing unit and the single sperm injection unit are all electrically connected with the main control module, and the operation method of the system comprises three steps of sperm capturing, ovum fixing and single sperm injection. According to the automatic ICSI system capable of accurately identifying and the operation method, the system can replace manual work to realize automation, is stable and reliable in experimental structure, adopts an AI image system to identify healthy and high-quality sperms and intelligently identify the spindle body part of an ovum, can perform needle insertion and injection on the best-quality sperms through the most appropriate position, greatly reduces the damage to the ovum, and the probability of various fertilization failures or embryo development potential underground caused by human factors is reduced to the greatest extent.