The desert plant Hedysarum scoparium uses leaflets and rachises as its photosynthetic organs. The abundance of leaflets was lower under unfavorable environmental conditions and higher with improved water conditions. To examine the characteristics associated with the adaptation of H. scoparium to its environment, we selected plants with both compound leaves and rachis without leaflets to study the anatomical structures and gas exchange characteristics of the two organs. The results show that the water storage tissues in rachises were more developed compared with the leaflets. The diurnal courses of the net photosynthetic rate for the rachis and the leaflet were both in a bimodal pattern. Meanwhile, both two peak values of the rachis were significantly higher than those of the leaflet. The daily average transpiration rate was significantly higher in the rachis than in the leaflet in order to lower the temperature of the rachises. It was concluded that under desert drought conditions, the leaflets of H. scoparium were partially or completely degraded to reduce the transpiration area as an adaptive response to water deficit, and only the rachises were retained as photosynthetic organ. The rachises were found to be better suited to a desert habitat than the leaflets.