Myopia is a growing global public health concern. Recent studies have revealed that the regulation of eye growth occurs via a complex signaling cascade, which originates in the retina and across the choroid to the sclera. Identifying key proteins and specific biological processes in the retina, choroid, and sclera is crucial for understanding the molecular mechanisms underlying myopia development. This study provides an in-depth proteomic and phosphoproteomic atlas of the retina, choroid, and sclera in guinea pigs with form-deprivation myopia, uncovering the potential molecular mechanisms driving the progression of myopia.