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Oxygen vacancy is known to play an important role for the physical properties in SrTiO₃(STO)-based systems. On the surface, rich structural reconstructions had been reported owing to the oxygen vacancies, giving rise to metallic surface states and unusual surface phonon modes. More recently, an intriguing phenomenon of a huge superconducting transition temperature enhancement was discovered in a monolayer FeSe on STO substrate, where the surface reconstructed STO (SR-STO) may play a role. In this work, SR-STO substrates were prepared via thermal annealing in ultra-high vacuum followed by low energy electron diffraction analyses on surface structures. Thin Nb films with different thicknesses (d) were then deposited on the SR-STO. The detailed studies of the magnetotransport and superconducting property in the Al(1 nm)/Nb(d)/SR-STO samples revealed a large positive magnetoresistance and a pronounced resistance peak near the onset of the resistive superconducting transition in the presence of an in-plane field. Remarkably, the amplitude of the resistance peak increases with increasing fields, reaching a value of nearly 57% of the normal state resistance at 9 T. Such resistance peaks were absent in the control samples of Al(1 nm)/Nb(d)/STO and Al(1 nm)/Nb(d)/SiO₂. Combining with DFT calculations for SR-STO, we attribute the resistance peak to the interface resistance from the proximity coupling of the superconducting niobium to the field-enhanced long-range magnetic order in SR-STO that arises from the spin-polarized in-gap states due to oxygen vacancies.