BACKGROUND: Prunella vulgaris L. is a medical plant cultivated in sloping, sun-shaded areas in China. Recently, owing to air-environmental stress, especially drought stress strongly inhibits plant growth and development, the appropriate fertilizer supply can alleviate these effects. However, these is little information about their effects on P. vulgaris growing in arid and semi-arid areas with limited water and fertilizer supply. RESULTS: In this study, water stress decreased the photosynthetic pigment contents, inhibited photosynthetic efficiency, induced photodamage in photosystem 2 (PS2), and decreased leaf instantaneous WUE (WUEi). The decreased net photosynthetic rate (Pn) under medium drought stress compared with the control might result from stomatal limitations. However, fertilizer supply improved photosynthetic capacity by increasing the photosynthetic pigment contents and enhancing photosynthetic efficiency under water deficit. Moreover, medium fertilization also increased WUEi under the two water conditions, but fertilizer supply did little to alleviate the PS2 photodamage caused by drought stress. Hence, drought stress was the primary limitation in the photosynthetic process of P. vulgaris seedlings, while the photosynthetic characteristics of the seedlings exhibited positive responses to fertilizer supply. CONCLUSIONS: Appropriate fertilizer supply is recommended to improve photosynthetic efficiency, enhance WUEi and alleviate photodamage under drought stress.