Even though Jerusalem artichoke (Helianthus tuberosus L.) has strong resistance to abiotic stresses, salinity can still reduce the biomass of Jerusalem artichoke. The purpose of this study was to elucidate the differences in the development of Jerusalem artichoke and the dynamics of sugar throughout the growth period under high (7.23–8.15 g/kg) and low (3.20–4.32 g/kg) salinity stress in the field in Jiangsu Province, China. This study confirmed that high salinity promoted the conversion of reducing sugars to non-reducing sugars (fructans) in Jerusalem artichoke tubers, but significantly reduced the biomass of Jerusalem artichoke and advanced the peak time of the dry matter accumulation of aerial parts. In addition, in the early and late stages of tuberization, the total sugar content of tubers under low salinity conditions (786 ± 8 mg/g and 491 ± 8 mg/g) was 93.3% and 1.15 times than those under high salinity conditions, respectively. Moreover, the total sugar content in stems was consistently greater under high than low salinity conditions in the same period. The accumulation rate and the amount of dry matter were significantly higher in stems than in other tissues. Therefore, the aerial parts of “Nanyu No. 1” could be harvested before mid-to-early October, and the tubers after mid-November. This study revealed the internal reasons for the decreased yield of Jerusalem artichoke under salt stress, and provided theoretical basis and guidance for the cultivation and utilization of Jerusalem artichoke in saline-alkali soil.