Docosahexaenoic acid (DHA) and ultra‐long‐chain polyunsaturated fatty acids (ULC–PUFAs) are uniquely enriched in membrane phospholipids of retinal photoreceptors. Several studies have shown that di‐DHA‐ and ULC–PUFA‐containing phospholipids in photoreceptors have an important role in maintaining normal visual function; however, the molecular mechanisms underlying the synthesis and enrichment of these unique lipids in the retina, and their specific roles in retinal function remain unclear. Long‐chain acyl‐coenzyme A (CoA) synthetase 6 (ACSL6) preferentially converts DHA into DHA–CoA, which is a substrate during DHA‐containing lipid biosynthesis. Here, we report that Acsl6 mRNA is expressed in the inner segment of photoreceptor cells and the retinal pigment epithelial cells, and genetic deletion of ACSL6 resulted in the selective depletion of di‐DHA– and ULC–PUFA‐containing phospholipids, but not mono‐DHA‐containing phospholipids in the retina. MALDI mass spectrometry imaging (MALDI–MSI) revealed the selective distribution of di‐DHA– and ULC–PUFA‐containing phospholipids in the photoreceptor outer segment (OS). Electroretinogram of Acsl6−/− mice exhibited photoreceptor cell‐derived visual impairment, whereas the expression levels and localization of opsin proteins were unchanged. Acsl6−/− mice exhibited an age‐dependent progressive decrease of the thickness of the outer nuclear layers, whereas the inner nuclear layers and OSs were normal. These results demonstrate that ACSL6 facilitates the local enrichment of di‐DHA– and ULC–PUFA‐containing phospholipids in the retina, which supports normal visual function and retinal homeostasis.