The invention discloses a second-generation sequencing method for dimolecular self-checking library preparation and hybrid capture used for trace DNA ultralow frequency mutation detection. The methodcomprises the following steps: extracting plasma free DNA, performing DNA chemical error repair, preparing a self-checking dimolecular identification code hairpin type joint, repairing plasma free DNA, connecting DNA with the joint, and performing Pre-PCR amplification, excessive hybrid capture, Post-PCR amplification, computer sequencing, data error correction, and mutation analysis and annotation. The method disclosed by the invention can efficiently realize low frequency mutation detection of plasma free DNA. DNA error repair and dual redundancy checking technology can enable the method tohave ultralow false positive rate and high sensitity while detecting trace samples, thus avoiding defects of existing plasma circulating free DNA detection methods, not only realizing cancer mutationdetection and targeted medication guidance, but also realizing early screening of genetic and birth defects of fetus.