This study used the stable and convergent Dufort-Frankel method to differentially discretize the diffusion equation of the ground-well transient electromagnetic secondary field. The absorption boundary condition of complex frequency-shifted perfectly matched layer (CFS-PML) was used for truncation so that the low-frequency electromagnetic wave can be better absorbed at the model boundary. A typical three-dimensional (3D) homogeneous half-space model was established and a low-resistivity cube model was analyzed under the half-space condition. The response patterns and drivers of the low-resistivity cube model were discussed under the influence of a low-resistivity overburden. The absorption boundary conditions of CFS-PML significantly affected the low-frequency electromagnetic waves. For a low-resistivity cube around the borehole, its response curve exhibited a single-peak, and the extreme point of the curve corresponded to the center of the low-resistivity body. When the low-resistivity cube was directly below the borehole, the response curve showed three extreme values (two high and one low), with the low corresponding to the center of the low-resistivity body. The total field response of the low-resistivity overburden was stronger than that of the uniform half-space model due to the low-resistivity shielding effect of electromagnetic waves. When the receiving-transmitting distance gradually increased, the effect of the low-resistivity overburden was gradually weakened, and the response of the low-resistivity cube was strengthened. It was affected by the ratio of the overburden resistivity to the resistivity of the low-resistivity body.