Leaf-color mutants are crucial germplasms for understanding the mechanisms of pigment metabolism and chloroplast development. In this study, to identify the mechanisms of temperature-sensitive albino phenotype in Brassica napus, physiological assessment and transcriptome analysis were performed in two resynthesized B. napus inbred lines, the green-leaf line G7097 and white-leaf line W7105. Under low temperature in field conditions, in albino leaves of W7105, the chlorophyll and carotenoid contents were dramatically decreased and chloroplast structure was abnormal. Compared with green leaves, albino leaves showed significantly lower net photosynthetic rate (Pn) and significantly higher intercellular CO2 concentration (Ci). Transcriptome analysis of leaves at three different developing stages was performed in G7097 and W7105 lines. After pairwise comparisons, a total of 1532 differentially expressed genes (DEGs) associated with leaf color phenotypes were screened out, including 540 up-regulated DEGs and 992 down-regulated DEGs. GO and KEGG enrichment analysis showed that the up-regulated DEGs in albino leaves of W7105 were significantly enriched in proteasome, translation process, carbohydrate and energy metabolism pathways; while the down-regulated DEGs were significantly enriched in chloroplasts, photosynthesis and electron transport chain. Moreover, several DEGs involved in chlorophyll and carotenoid biosynthesis were significantly down-regulated in albino leaves from W7105, suggesting that chlorophyll and carotenoid metabolisms were also impaired in albino leaves. These findings provide a foundation for mapping the candidate genes and understanding the molecular mechanisms of albino leaves in B. napus.