Confirmed to be a new type of food resource, quail egg can provide humans with high-quality protein and offer various nutrients that can promote growth and development. Post-translational modification of proteins can regulate their molecular structures and physiological functions. However, the understanding and related research of quail egg holoproteins and post-translationally modified proteins is not yet sufficient. This study provides an in-depth analysis of quail egg proteins using an omics strategy. A total of 175 proteins, 109 N-glycoproteins (293 N-glycosylation sites) and 23 phosphoproteins (84 phosphorylation sites) were identified. Motif analysis showed that N-glycosylation sites of quail eggs were classical sites. The main characteristic sequence of the phosphorylation site is “S-X-E” (77%). Functional analysis indicated that quail egg proteins, modified proteins were enriched in the regulation of enzyme activity. These results have significant reference value for understanding the structure, function of quail eggs, explaining the physicochemical reaction during the storage.