Objective：To identify the expression of endogenous peptides during development of zebrafish and their relationship with eye development. Methods：The zebrafish embryos were collected for 0 hour and 48 hours respectively for peptide mass spectrometry analysis. The differential peptides in the development process were screened for bioinformatics analysis to detect the relationship with eye development. Results：A total of 232 bands of differential peptides were screened. Analysis of physical and chemical properties found that the molecular weight is distributed below 2 000 Da，isoelectric point of proteins mainly weak acid and weak alkaline，isoelectric point of little protein is neutral. Bioinformatics analysis found that Vitellogenin（VTG），Titin（TTN） encoded precursor protein have large numbers of peptides. The molecular function and physiological function of all differential peptides were analyzed by ingenuity pathway analysis（IPA），which found they are closely related embryonic development. The signal pathway analysis revealed that axonal-mediated signaling pathway，FAK signal pathway and MAPK signal pathway related to eye development. Conclusion：The differential endogenous peptides of zebrafish embryo development are stable，closely related to embryonic development，and may affect eye development through related signal pathway，which will provide new research ideas and mechanism for eye development.