The invention discloses a high-temperature combined method for extracting genomic DNA of fish enteric microorganisms. The high-temperature combined method includes the steps that firstly, the walls of various fish enteric microorganisms are properly broken through a lysozyme method and an ultrasonic method at the same time, wherein the ultrasonic physical wall breaking condition ranges from 150 w to 250 w, ultrasonic treatment is carried out for 2-3 s and then carried out again after an interval of 5 s, and the process is repeated 50-60 times; secondly, the sample obtained after ultrasonic treatment and lysozyme are jointly incubated for 30 min in a water-bath constant-temperature oscillator at the temperature of 55-65 DEG C, and the mixture and RNase A are jointly incubated at the temperature of 27-32 DEG C. According to the method, the walls of the various microorganisms are properly broken under the proper and mild ultrasonic condition, and the genomic DNA is prevented from being broken and degraded. As the specific temperature range for incubating the lysozyme and the sample and the specific temperature range for incubating the RNase A and the sample are set, the splitting decomposition effect of the lysozyme can be improved, and it can be avoided that the genomic DNA is degraded by DNA enzymes in tissues and cells. Operation is easy, the extracted genomic DNA is complete and low in degradation rate, and the fish enteric microorganism structure can be truly reflected by the types of the microorganisms identified according to the extracted DNA.