As sessile organisms, plants face a wide range of abiotic stresses, with salinity being a prominent constraint affecting their growth, development, and productivity, particularly in arid and semi-arid regions. This study focused on understanding how salinity impacts Jatropha curcas, an important oilseed plant for biodiesel production. By examining the anatomy and ultrastructure of stomata and chloroplasts, we investigated the effects of prolonged salinity stress on J. curcas. This stress led to changes in stomatal density, stomatal index, and ostiole aperture, which case an imbalance of water conductivity in the xylem. Through transmission electron microscopy, we explored the subcellular organization of J. curcas chloroplasts and their contribution to plant photosynthetic efficiency, providing insights into their role in this process. Notably, salinity treatment resulted in a significant increase in starch granules accumulation, leading to impaired the granal and stromal grana lamellae, destroying this ultrastructure. Our findings indicate that the anatomy and ultrastructure of chloroplasts play a crucial role in influencing photosynthetic efficiency and hydraulic conductivity. This study offers new perspectives on the structure and function of chloroplasts in J. curcas, presenting innovative opportunities to develop strategies that enhance biofuel production in areas with high soil salinity.