In this paper, using three-dimensional porous alumina (3D-AAO) as a template, Ni-Zn-In nanowires array with periodically changing diameters was successfully prepared by direct current electrodeposition method. The effect of deposition voltage on the morphology, crystal structure and magnetic properties of Ni-Zn-In ternary alloy nanowires was studied. The experimental results show that the diameters of the nanowires are 212 nm and 151 nm, and the periodic length is 800 nm, which matches the pore size of the phosphoric acid-etched 3D-AAO template. XRD results indicate that the crystal structure of Ni-Zn-In nanowires can be adjusted by the deposition voltage. The VSM results reveal that the Ni-Zn-In nanowires possess soft magnetic properties and significant magnetic anisotropy, with the easy magnetization direction parallel to the film. The nanowires deposited at −1.5 V exhibit the highest coercivity of 161 Oe and squareness of 0.045. Micromagnetic simulations show that the magnetization reversal mechanism of the Ni-Zn-In nanowires is localized nucleation mode.