The invention provides infectious hematopoietic necrosis (IHN) nucleic acid vaccines for Chinese rainbow trout and application thereof. A preparation method of the IHN nucleic acid vaccines for Chinese rainbow trout includes the following steps that firstly, specific primers for amplifying genotype J IHN virus surface glycoprotein genes (Glycoprotein, G) are designed; secondly, IHN virus isolates are cultured with a virus sensitive cell line, and then virus genome RNA is extracted; thirdly, the virus genome RNA obtained in the second step is subjected to one-step RT-PCR amplification with the primers obtained in the first step; fourthly, a recovery product obtained in the third step is connected with a pMD19-T simple vector, a connection product is converted into DH5alpha competent cells, single colonies are picked out, plasmids are extracted for PCR identification after amplified culture, and plasmids identified to be correct are subjected to sequencing; fifthly, IHNV isolate glycoprotein genes identified to be correct in the fourth step are cloned to a eukaryotic expression vector pcDNA3.1 with BamH I and Xho I restriction enzyme cutting sites to establish the nucleic acid vaccines.