Zirconium tanning agent, which is mainly composed of low-toxic tetravalent zirconium (Zr4+) salts, has been considered the most promising eco-friendly tanning agent for leather manufacturing, due to its comparable tanning performance with trivalent chrome. However, in the initial penetration stage of the zirconium tanning process, macromolecular multinuclear complexes are commonly formed because of the rapid coordination between hydrated Zr4+, which can easily cross-link with active groups of neighboring collagen fibers and thus block subsequently even penetration of zirconium tanning agents, resulting in surface over-tanning and ununiform tanning effects. Herein, to address the aforementioned issues of conventional zirconium tanning, inert-surface modification of collagen fibers was proposed by using PEGylated epoxy copolymers (PEGMA-co-GMA, defined as PPG) to pretreat bated hide, based on the covalent reactions and hydrogen-bond interactions of PPG with amino and carboxyl groups on collagen fibers, respectively. After modification, the surface reactivity of skin collagen was significantly reduced, which was able to delay the cross-linking interactions with zirconium tanning agents and thus promote uniform penetration. Simultaneously, the extra hydroxyls produced from the ring-open reactions of epoxy groups could also mitigate the excessive coordinated complexation of hydrated Zr4+, leading to efficient penetration of zirconium tanning agents. Compared with conventional zirconium tanning, research results showed that this inert-surface modification strategy could comprehensively improve the overall leather performance with both efficient and uniform tanning effects. Moreover, the resultant leather qualities, including thermal stability, physical and mechanical properties, and organoleptic properties, are very comparable with chrome-tanned leather. In addition, attributing to the reaction between collagen amino and PPG, the use of sodium chloride was avoided, resulting in a cleaner salt-free pickling process. Altogether, this inert-surface modification strategy represents a significant step forward for effective and cleaner tanning technology, which will accelerate the wide application of Zr(IV) in place of traditional chrome tanning agents.