To better understand the mechanism of inherent salt resistance in Jerusalem artichoke (Helianthus tuberosus L.), physiological and metabolic responses of tubers at the initiation stage of sprouting under different salt stress levels were evaluated in the present study. As a result, 28 metabolites were identified using proton nuclear magnetic resonance (1H-NMR) spectroscopy. Jerusalem artichoke tubers showed minor changes in metabolic response under moderate salt stress when they had not yet sprouted, where metabolism was downregulated at the start of sprouting and then upregulated significantly after plants became autotrophic. However, mild and severe salt stress levels caused different metabolic response patterns. In addition, the accumulation of fructose and sucrose was enhanced by moderate salt stress, while glucose was highly consumed. Aspartate and asparagine showed accelerated accumulation in sprouting Jerusalem artichoke tubers that became autotrophic, suggesting the enhancement of photosynthesis by moderate salt stress.