Previous studies on the biomarkers of pathologic myopia choroidal neovascularization (pmCNV) development merely detected limited types of proteins and provide a meagre illustration of the underlying pathways. Hence, an intact picture of molecular changes in the aqueous humor (AH) of pmCNV patients is lacking. Here, to explore the potential mechanisms and biomarkers of pmCNV, we analyzed the correlation between atrophic (A) lesions and neovascular (N) lesions in a myopic cohort based on the ATN grading system for myopic maculopathy (MM). In a quantitative proteomics test of AH profile of our patients, a significant correlation was found between A and N lesions (R = 0.5753, P < 0.0001). Accordingly, groups were divided into patients without MM, patients with myopic atrophic maculopathy (MAM), and patients with pmCNV (N2a lesion). In proteomics analysis, the existence of GFAP and complement-associated molecules in AH samples of the 3 groups also supported that MAM and pmCNV shared similar characteristics. Analyses of the differentially expressed proteins between the pmCNV group and two controls were performed. We identified several potential biomarkers for pmCNV, including FCN3, GFAP, EGFR, SFRP3, PPP2R1A, SLIT2, and CD248. Taken together, our study provides new insights for further research on pmCNV development.