The invention discloses a design principle of a nucleic acid amplification blocking agent for detecting low-abundance mutant sequences, and relates to the field of detection of mutant genes. The nucleic acid amplification blocking agent is oligonucleotide modified by locked nucleic acid (LNA), and a pairing region of the nucleic acid amplification blocking agent is located between amplification sequences and completely paired with wild-type gene sequences, and has at least one mispairing with the mutant sequences. The invention further discloses application of the nucleic acid amplification blocking agent in detecting the low-abundance mutant sequences. According to the nucleic acid amplification blocking agent and the application, the affinity between the nucleic acid amplification blocking agent modified by locked nucleic acid and the mutant nucleic acid sequences / wild-type nucleic acid sequences has a huge difference, and the purpose of highly-selective amplification / enrichment of the mutant sequences in a sample is achieved; the nucleic acid blocking agent has the advantages of being high in affinity, flexible in basic group modification position, good in heat stability, cheapin price and the like, and has a more significant detection effect on deletion mutation and insertion mutation.