Although cell-encapsulating hydrogels are of tremendous interest in regenerative medicine, few of them have been used in clinics and rarely used natural extracellular matrices as polymer precursors. One successful example is to use riboflavin (RF)/ultraviolet A (UVA) to cross-link corneal collagen, which has been used in clinics to halt disease progression in patients with corneal ectatic diseases. However, high-energy UVA and its action on RF cause tissue damage, particularly irreversible endothelium loss, and thus standard RF/UVA protocol may have limitations in treating patients at the advanced stage with thin cornea. Photo-initiators lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) has high efficiency under visible 405 nm light, and is widely applied in 3D bioprinting to cross-link synthesized monomers. Here, we introduced a new strategy to cross-link cornea using LAP and visible light (VL). The LAP/VL protocol could effectively increase corneal stiffness with equivalent efficiency to the RF/UVA protocol in both porcine and rabbit cornea. As LAP and VL were used, the loss of corneal endothelial and stromal cells was minimized, and epithelial wound healing and stromal cell repopulation were accelerated. In summary, we propose that the LAP/VL protocol is an effective and safe alternate for cornea CXL with advantages for relatively thin cornea. Our study also expands the application scope of LAP, indicating it is a suitable photocatalyst for natural extracellular matrices CXL.