Eggs are the best protein supplements for human beings, which have high nutritional value and are rich in all kinds of essential amino acids. Wild eggs are produced by some rare poultry, considered to have higher nutritional value than ordinary eggs. In this study, black-bone chicken and ring-necked pheasant eggs were selected as samples. Isobaric tags for the relative and absolute quantification labelling techniques (iTRAQ) were used to analyze the protein difference between the two samples. A total of 205 proteins were identified, of which 87 were significantly different. Among those differential proteins, 37 were significantly up-regulated while 50 were significantly down-regulated. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these differentially expressed proteins were closely related to cholesterol metabolism. The expression of some proteins that are adverse to cholesterol metabolism was significantly down-regulated in black bone chickens, such as Apolipoprotein B, Apovitellenin-1, Vitellogenin-1 and Vitellogenin-2. Protein interaction analysis showed that there were strong interactions among these proteins. These results indicated that compared with ring-necked pheasant, black-bone chicken eggs have a stronger ability to metabolize cholesterol and are less likely to cause the increase of plasma cholesterol.