Wild jujube (Ziziphus acidojujuba) and cultivated jujube (Ziziphus jujuba) belong to the family Rhamnaceae. Jujubes have marked drought- and salt-tolerant properties. After salt stress, wild jujube seedling growth was inhibited and photosynthetic efficiency was reduced. A bioinformatics approach was used to analyze the transcriptomics data from wild jujube seedlings grown under salt stress, and the genes differentially expressed under the salt stress were identified to provide a theoretical basis for the development and use of wild jujube plantations in salinized soil. The transcriptome sequencing from leaves of wild jujube seedlings was carried out using second-generation sequencing technology. The effects of salt stress on the differential expression of photosynthesis-related genes in wild jujube seedlings were analyzed. Transcriptome sequencing revealed a total of 5269 differentially expressed genes (DEGs), of which 2729 were up-regulated and 2540 were down-regulated. DEGs were mainly enriched with respect to photosynthesis, photosynthetic antenna proteins, glyoxylic acid and dicarboxylic acid metabolism, linolenic acid metabolism, cysteine and methionine metabolism, and porphyrin and chlorophyll metabolism. Among them, the photosynthesis pathway-related DEGs were most highly enriched. Further analysis of porphyrin and chlorophyll synthesis and photosynthesis-related pathways revealed that they were significantly enriched by 97 photosynthesis-related DEGs. The DEGs in the photosynthesis and photosynthetic antenna protein pathways were down-regulated, whereas the DEGs glutamyl-tRNA reductase (HEMA), ferrochelatase (HEMH), and pheophorbide a oxygenase (PAO) in the porphyrin and chlorophyll synthesis pathways were up-regulated, with the remainder being down-regulated. The nuclear gene encoding Rubisco, the key enzyme in the photosynthetic carbon fixation pathway, was also down-regulated. The results showed that the photosynthetic rate of wild jujube seedlings decreased following exposure to salinity stress, an effect that was related to the increased synthesis of 5-aminolevulinic acid and heme, and the up-regulation of expression of a gene encoding a chlorophyll-degrading enzyme, and was related to the down-regulation of gene expression in photosynthesis-related pathways such as light energy capture and carbon fixation. Selection of nine DEGs related to photosynthesis and chlorophyll biosynthesis by quantitative real-time-PCR confirmed that expression changes of these nine DEGs were consistent with the transcriptome sequencing results.