The invention discloses a method for separating long terminal repeats of retrotransposons. Genome DNA is taken as a template, an RNaseH1 primer is respectively combined with different annealing control primers for first polymerase chain reaction (PCR) reaction, the first PCR product is diluted to serve as a template, an RNaseH2 primer and a universal primer UP are subjected to secondary PCR reaction amplification, conversion and extraction of plasma DNA are performed, and a sequence is subjected to sequencing to obtain an amino acid sequence of RNaseH enzyme, and proteins are encoded. Compared with the common PCR technology, the method has the advantages that: the operation is simple, long terminal repeat regions of the retrotransposons are easily aligned, and the pertinence is high; compared with a flow type magnetic microbead inverse hybrid method, the method has the advantages of saving hybrid, eluting, screening and other processes, simplifying the flow and having high efficiency;and compared with other separation methods, the method has the advantages of reducing time consumption, quickly obtaining target segments, cloning the long terminal repeats in short time, and reducing false positive rate.