The invention discloses a method for simulating a target disease simulating sequencing library and application thereof, wherein the method for simulating the target disease simulating sequencing library can obtain different system and embryonal system variation characteristics, a hybrid/pure ratio and different disease affecting sequence purities according to the requirement, thereby simulating offline data in a capturing sequencing condition in a targeted manner. Furthermore the method can simulate whole-genome offline data and can simulate capturing sequencing offline data, thereby realizingwide application range. Furthermore the method realizes relatively high operation speed and can generate a required analog sequence in a relatively short time period. Furthermore high simulation degree of the simulated sequence is realized.