The invention discloses a method for performing variation simulation on a sequencing sequence and application thereof, wherein the method for performing variation simulation comprises the steps of acquiring a base sequence of a to-be-simulated area; performing variation state marking on the base sequence so as to obtain a marked characteristic string; selecting a to-be-added variation; integratingthe to-be-added variation with the marked characteristic string so as to obtain the characteristic string after variation adding; and performing base reduction on the characteristic string after variation adding so as to obtain the sequence after variation simulation. According to the method, through marking the variation state of the base sequence, the variation type of the base is set, therebysimulating various variations. A simple variation simulating method and high generating speed are realized. Furthermore a specific variation combination can be designed according to the requirement for testing. Furthermore high simulation degree of the sequence after variation simulation is realized.