Fe dopants on the surface of a Bi2Te3 thin film grown on a superconducting NbSe2 substrate by molecular beam epitaxy are investigated by a dilution-refrigerator scanning tunneling microscope. Utilizing the tip-induced band bending effect, we precisely manipulate the dopant’s energy level and charge state. When the dopant level is tuned near the superconducting gap, the system reaches the mixed valence regime. Yu-Shiba-Rusinov states emerge, shift continuously, and cross zero energy as the dopant level is tuned, all of which are reproduced by our multi-orbital Anderson-Kanamori model simulations. Unlike conventional exchange-coupling-driven transitions of Yu-Shiba-Rusinov states where Kondo screening dominates, the mechanism here is governed by dopant-level-driven charge transfer and resonantly enhanced Kanamori interactions. These findings open a new avenue to quantum state engineering and spin-dependent transport in semiconductor/superconductor hybrid systems.