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Background: Jerusalem artichoke (Helianthus tuberosus L.) is moderately tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, gene transcription is likely to undergo large changes. Previous studies have hinted at the importance of temporal expression analysis in plant transcriptome research. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h (hour), 6 h, 12 h, 24 h, and 48 h, with 150 and 129 unigenes and 9023 DEGs (differentially expressed genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among them. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belonging to PYL (abscisic acid receptor PYR/PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (genes such as jasmonate ZIM-domain gene), and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qRT-PCR of 12 randomly selected and function known genes confirmed the accuracy of RNA-seq. Conclusions: Under the influence of high salinity (300 mM) environment, Jerusalem artichoke suffer serious damage in a short period of time. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, and the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern. Research emphasized the regulatory role of hormones under high salt shocks and provided an explorable direction for the study of plant salt tolerance mechanisms.