The invention discloses a method for separation, dispersion and sequence repetition of a bead-probe complex. The method comprises the following steps: firstly, the preparation of a genome fragment enriched library, which is to perform restriction enzyme digestion on a genome, to recover fragments with adequate dimensions, to add linkers on T4 ligase, and to perform cyclic amplification of the genome fragment library after restriction enzyme digestion through PCR of a small number of linkers; secondly, the preparation of the bead-probe complex, which is to realize biotin labeled DNA probes by the primer amplification method, and to bind biotin labeled single-chain probes on beads; and thirdly, acquisition of a target fragment group, which is to perform crossover on the bead-probe complex and the genome library, to acquire a target fragment, to separate and clone the target fragment, and to perform positive selection on the target fragment. The method is simple, high-efficiency and quick, shortens the experimental period, reduces the cost consumption, greatly improves the efficiency, and does not require special experimental equipment.