To investigate alterations of lipidomes in the progress of photoreceptor degeneration induced by N-methyl-N-nitrosourea (MNU) in a rat model, retinal lipid molecular species in adult Sprague–Dawley (SD) rats at 1, 3, and 7 days after MNU administration and age-matched controls were analyzed by the shotgun lipidomics technology. Moreover, total fatty acid levels in retinal, liver, and plasma samples of different groups were determined with gas chromatography. Generally, at day 1, the levels of ethanolamine plasmalogen species in retinas were markedly elevated after treatment with MNU, while the contents of other phospholipids and sphingolipids in the retina were not significantly changed than those of the control group. The compositions of almost all of unsaturated fatty acids in the retina increased significantly at day 1 after MNU administration. At day 7, the MNU treatment group has significant increases in lipid species in the retina. However, the majority of lipids containing docosahexaenoic acid (DHA, 22:6n-3) and docosapentaenoic acid (22:5n-6) declined, especially di-DHA phospholipids were dramatically reduced in the retina. In contrast, similar alterations did not occur in plasma or the liver after MNU treatment. These results suggested that at the early stage of photoreceptor degeneration, lipidome remodeling in the retina might involve protection of photoreceptor from apoptosis and continue their transduction of light. However, at the late stage of photoreceptor apoptosis, increases in comprehensive lipid species occurred, likely due to the myelination of the retina. Finally, the deficiency of DHA in photoreceptor degeneration could exacerbate the influence of myelination on retinal function. We further investigated the effects of unsaturated fatty acids on neuronal apoptosis. The preliminary experiments confirmed our observation from lipidomics analysis that unsaturated fatty acids can protect neurons from apoptosis. Collectively, our study suggests that increased levels of DHA should be protective from photoreceptor degeneration.