Myopia is a growing global public health concern. The retinal–choroid–sclera (RCS) signalling cascade is crucial in regulating eye growth and is influenced by visually induced signalling. Understanding the molecular mechanisms underlying this cascade is vital to identify therapeutic targets for myopia. This study provides an in-depth proteomic and phosphoproteomic atlas of the RCS in guinea pigs with FDM, uncovering the potential molecular mechanisms driving the progression of myopia.