In order to improve the corrosion resistance of implant materials and understand the corrosion mechanisms, we prepared a biomedical Nb-Zr alloying layer on 316L stainless steel using double-layer glow plasma surface-alloying technology and investigated the effects of gas pressures on its surface structure, mechanical properties, and corrosion behavior. In particular, the surface states of the substrate and alloying layers were investigated using 3D confocal micrographs, the water contact angle, and UV reflectance, which aims to study the effect of the surface quality on corrosion resistance and discuss the corrosion mechanisms. The results show that the working pressure has an effect on the current density, the sputtering amount of the alloying elements, and the diffusion process of the alloying elements during glow discharge. The Nb-Zr alloying layer prepared under a pressure of 40 Pa had a uniform and dense surface structure, and the distribution was island-like. A Nb-Zr alloying layer with a thickness of 15 μm was successfully obtained, including the diffusion layer and the deposition layer. Simultaneously, the elements Nb and Zr were gradually distributed along the depth, and a high Nb concentration formed in the Nb-Zr alloying layer. The solid solution formed by Zr in the Nb layer significantly improved the microhardness and corrosion resistance of the substrate. The Nb-Zr alloying layer prepared under a pressure of 40 Pa had the lowest corrosion current density and excellent corrosion resistance, which originated from the passive film formed by the Nb-Zr alloying layer that could inhibit the invasion of corrosive ions and improve the corrosion resistance. In addition, the Nb-Zr alloying layer could promote cell proliferation during long-term use and had good biocompatibility. Our study provides an efficient, high-quality processing method for the surface modification of biomedical metallic materials to form thicker Nb-Zr alloying layers as a cost-effective alternative to bulk Nb-based alloys.