The purpose of the study is to ascertain the molecular mechanism of the albino mutation of Aristaloe aristata, screen related functional genes, and provide basis for the breeding. The Illumina HiSeq sequencing platform was used to carry out transcriptome high-throughput sequencing for normal leaf color seedlings WT, albino mutant ls and qj. The sequencing results were annotated and analyzed. A total of 67.72 Gb clean data was obtained. A total of 122 665 unigene annotation results were obtained from functional annotation. For the analysis of Unigenes expression, a total of 914 differentially expressed genes (DEGs) in ls were screened out, among them, 453 genes were up-regulated and 461 down-regulated. There were 1851 differentially expressed genes (DEGs) screened in qj, of which up- and down-regulated genes were 868 and 983, respectively. According to a comparative analysis of GO functional enrichment and KEGG metabolic pathway, it was found that in the two mutant strains, there were many DEGs enriched in pigment accumulation, cell wall organization or biogenesis, cell wall, cell periphery, hydrolase activity of hydrolyzing o-glycosyl compounds, hydrolase activity acting on glycosyl bonds, and biosynthesis pathway of secondary metabolism, while the DEGs related to photosynthesis were not significantly enriched. In the pathway related to photosynthesis, the expression of porA and cab13 were significantly down-regulated in mutant ls, and porA and moda were significantly down-regulated in mutant qj. The results of real-time reverse transcriptase PCR (qRT-PCR) confirmed the consistency of the relative expression trend and the transcriptome data of these genes. The expression of the key gene, porA, which was down-regulated in both mutants, was assumed to be a key factor in the formation of albino seedlings of A. aristate since it was found to affect the enzymatic reaction of protochlorophyllin ester to chlorophyllin ester and thereby affecting the chlorophyll synthesis of the two mutants. Our study explored the transcriptome information of albinism mutation of A. aristate, screened the key genes with significant expression differences, and would provide an important theoretical basis for further exploring the molecular mechanism of albinism mutation of A. aristate.