Amorphous alloys have become a research hotpot in the field of materials science due to their unique long-range disordered structure and excellent physical properties. However, the complex microstructural evolution and electronic transport mechanisms of amorphous alloys under thermal effects still need in depth investigating. In this work, Ni₄₀Fe₃₅B₁₅Si₇P₃ and Ni₅₀Fe₂₅B₁₅Si₇P₃ amorphous alloy ribbons are prepared by the melt-spinning technique, and the as-cast samples are subjected to annealing treatments within the supercooled liquid region. The results show that annealing within the supercooled liquid region enhances the short-range order, reduces the free volume, and increases the atomic packing density of the alloys. The volume fractions of the local quasi-crystalline clusters in the annealed samples increase to 26%－34%. Furthermore, the increases in scattering centers and the release of internal stresses induced by the supercooled liquid region annealing lead to an increase in the electrical resistivity of the alloys. Specifically, the resistivity of the Ni₄₀Fe₃₅B₁₅Si₇P₃ alloy increases from 131.8 μΩ·cm to 217.0 μΩ·cm, a increase of 64.6%. Under an applied magnetic field, the deflection of electron trajectories due to the Lorentz force and the magnetostriction effect further increases the resistivity of the alloys. Additionally, thermal activation releases the bound electrons and enhances their scattering, resulting in an increase in the carrier concentration and a decrease in the carrier mobility of the annealed alloys. This study demonstrates that annealing can effectively control the short-range order and free volume distribution of amorphous alloys, thereby influencing their electronic transport properties. The findings provide an experimental basis for designing high-performance amorphous alloy electronic devices.