The invention relates to the technical field of gene knockout, and particularly discloses a method for selectively breeding bai2 gene deletion zebra fish through gene knockout. Through a CRISPR/Cas9 gene editing technique, suitable targeting loci are designed on a bai2 gene of the zebra fish, specific gRNA synthesized in vitro enters a cell of the zebra fish in a micro-coinjection mode, after embryo culture is conducted for 50 h, genotype analysis is conducted by selecting embryos, and thus the effectiveness of the selected loci is verified. According to the method, specific genes can be silenced more efficiently and more precisely in a living body genome, manufacturing is easy, the cost is low, the multiple loci on the target gene can be sheared simultaneously, and the any number of single genes are silenced; and expression of the bai2 gene is interfered, the function of the bai2 gene is studied in a genetics mode, the whole process of cardiac morphology generation and the molecular mechanism of adjusting and controlling the processes are further disclosed advantageously, and the method is of great significance to understanding of pathology of cardiac diseases in medicine and development of new treatment schemes.