The invention relates to a multi-target-point editing system and application thereof. The multi-target-point editing system comprises (a) and (b), wherein (a) represents Csy4 protein and Cas9 protein, and (b) is obtained by connecting two or more pieces of sgRNA to a Csy4 cutting and recognition sequence in series at intervals. According to the multi-target-point editing system and application thereof, the Csy4 protein and the corresponding recognition sequence thereof are applied to a CRISPR/Cas9 system for the first time, corresponding RNA sequences can be cut and recognized with the Csy4 protein, then the multiple pieces of sgRNA can be cut into independent fragments after being transcribed in the same expression cassette at the same time, and multi-target-point editing of genomes is achieved; meanwhile, the single-target-point cutting efficiency is obviously improved compared with that of a tRNA shearing system in the prior art, and the efficiency of detecting fragment deletion caused by multi-target-point cutting is higher than that of the tRNA shearing system.