• The Jerusalem artichoke genotypes which are able to maintain a high net photosynthesis rate under long terminal drought conditions led them to high inulin yield. • SPAD chlorophyll meter reading traits mainly contribute to high inulin content under short terminal drought conditions in HEL256, JA37, JA60, and JA125. • Jerusalem artichoke genotypes with performing high inulin content would be positive for sustainable improvement of drought tolerance under different durations of terminal drought.. Different terminal drought durations might impact inulin traits of Jerusalem artichoke (JA) and some physiological traits are expected to be relevant to their genotype response. Therefore, the aims of this study were to investigate the effect of different durations of terminal drought on inulin content and inulin yield as well as the associations among inulin traits, net photosynthesis rate (P n ), and SPAD chlorophyll meter reading (SCMR) in JA genotypes. The field experiment was designed as a split-plot design with four replications during the late-rainy seasons over two years (2017/18 and 2018/19). The main plots were three water levels composed of optimal conditions (SD0), short (SD1), and long (SD2) durations of terminal drought. Six JA genotypes (HEL256, JA37, HEL253, JA4, JA60, and JA125) were arranged in subplots. All genotypes showed that inulin content in tubers was clearly significantly increased, whilst inulin yield drastically decreased under different terminal drought durations in comparison with optimal conditions. Among six genotypes, only HEL256, JA37, JA60, and JA125 had high inulin content coupled with high P n under SD0, and they had high inulin content under SD1, mainly due to high SCMR. JA37, JA4, JA60, and JA125 had a high inulin yield under SD2, might be they had high P n , indicating that these genotypes could be used as potential parental lines through plant breeding programs for the improvement of new varieties suitable for growing in terminal drought prone-areas. Based on data for two years, inulin content had significant positive associations with P n ( p < 0.01) and SCMR ( p < 0.05) under SD0 and SD1, respectively. Inulin yield showed significantly ( p < 0.05 for 2017/18 and p < 0.01 for 2018/19) positive associations with P n under SD2, these results indicated that selection genotypes with high P n and SCMR could be effective as an indirect selection in acquiring high inulin traits simultaneously. Finally, our results suggest that SCMR could be used as a surrogate trait as it is a simple tool for drought-tolerant genotype screening in JA in order to identify high inulin content in tubers under short terminal drought durations.