Development of a water-efficient irrigation system is essential in order to cultivate Jatropha curcas, a bioenergy crop, in semiarid regions. In the present study, to determine the useful parameter for the efficient irrigation system, jatropha plants were grown in pots and root boxes under greenhouse conditions in Okinawa, Japan. At 6 to 9 months after transplanting, we measured the gas exchange rate during ongoing soil water deficits and attempted to identify the threshold of soil matric potential (pF) with changes of both intrinsic water use efficiency (A/gs) as a stomatal-based index and carboxylation efficiency (A/C i) as an index of non-stomatal limitation. When irrigation was stopped, A and gs began to decline, with each parameter reaching zero at pF 4.0. However, gs was more sensitive to soil water deficits than A. After re-watering, stomatal openings and carbon uptake recovered to the value observed before water stress treatment. At pF 3.5 and higher values (representing more severe water stress), A/gs intended to increase and A/C i sharply decreased. These results suggested that approximately pF 3.5 in the soil was the threshold of non-stomatal limitations to photosynthetic rate and should be useful to the re-watering point for the water-efficient irrigation system in jatropha.