The invention relates to a method and a device for simulating a target sequence, and electronic equipment. The method comprises the following steps of: acquiring a reference sequence and a to-be-fitted sequence; based on the reference parameters of the reference sequence corresponding to bases of a target sequence and the reference parameters of the to-be-fitted sequence to obtain the comparison parameters of the bases, wherein the reference parameters of the to-be-fitted sequence are obtained based on the multiple bases; determining whether the bases are qualified or not based on the comparison parameters to obtain qualified bases and unqualified bases; performing iterative subtraction on the comparison parameters of the unqualified bases to obtain target parameters, wherein the number ofiterations of iterative subtraction is based on the comparison parameters, and each iterative subtraction is associated with at least one comparison parameter of at least one base; and determining the simulated sequence of the target sequence based on the target parameters of the qualified bases and the unqualified bases. Therefore, parameter fluctuation of real targeted capture sequencing data can be simulated, and the simulated data is closer to reality.