No natural habitat of Sedirea japonica has been found in Korea for the past 20 years. This study was conducted to provide basic physiological data for the conservation strategy of this endangered plant in response to climate change. Soil fruit daylight system (SFDS) chambers were used and four treatment groups (2.6LVPD, 2.6HVPD, 8.5LVPD, and 8.5HVPD) were designed based on the RCP scenario (RCP 2.6, and 8.5) and VPD conditions (low VPD; LVPD, and high VPD; HVPD). Air dryness was induced in the HVPD groups during the daytime by increasing the atmospheric vapor pressure deficit (VPD). There was no significant difference based on the RCP scenario. However, the difference between LVPD and HVPD was considerable. Total CO2 uptake and transpiration were lower than those of LVPD due to the duration decrease of Phase I in 2.6HVPD and 8.5HVPD. There was a reduction in total biomass, leaf thickness, length, and the number of leaves. ABS/RC, DI0/RC, φD0, VK, VJ, and other chlorophyll fluorescence markers increased. φP0, RE0/RC, φE0, ψE0, φR0, RC/CS0, Sm, N, PIabs, DFabs, SFIabs, and PIabs,Total declined. Daily drought stresses impact the physiological mechanisms occurring at nighttime. The defense mechanisms against drought stress occur by conserving water by controlling the stomata, inactivating the reaction center, and increasing the dissipated energy through heat. In summary, S. japonica is flexible against drought stress.