Here, we presented an atlas of region resolved proteome and lipidome of mouse eye. The multiphoton microscopy-guided laser microdissection combined with in depth label-free proteomics, enable us to identify 13,536 proteins in 11 regions of mouse eye. Further integrative analysis of label-free proteome and imaging mass spectrometry (IMS), visually revealed the distinctive molecular features, including proteins, lipids, and glycans of various anatomical mouse eye regions. This work presented the panoramic eye proteome map, and served as the rich resource for eye researches in the future.