The frequent occurrence of monsoon winds usually leads to the formation of inverted soybean leaves. However, the effect of leaf inversion on photosynthetic capacity remains unclear. The responses of leaf anatomical traits, chlorophyll fluorescence induction kinetics parameters, photosynthetic capacity, and nonstructural carbohydrates of fully expanded leaves to inversion of leaves in two soybean cultivars were studied. Leaf inversion decreased the stomatal size and thickness of developed leaves. The net photosynthetic rate was significantly reduced under leaf inversion, which resulted from reduced excitation energy trapping and electron transport of PSII reaction center. Leaf inversion increased leaf temperature 10 d after leaf inversion but reduced the instantaneous water-use efficiency compared to normally oriented leaves. Due to the decreased light-saturated net photosynthetic rate, the soluble sugars of light-sensitive cultivar decreased significantly. In summary, leaf inversion deactivated the PSⅡ reaction centers, reduced photosynthesis and nonstructural carbohydrates in upper canopy soybean leaves.