Leymus chinensis is a perennial rhizomatous clone plant. It exhibits strong rhizomatous tillering and clonal growth through asexual reproduction. The root system is interdependent with aboveground growth and root growth can regulate aboveground growth and photosynthesis. Melatonin has been shown to regulate root growth and promote photosynthesis. However, it remains unclear whether melatonin affects aboveground growth and photosynthesis by regulating rhizome growth. To address this gap, we studied nine Leymus chinensis from different geographical locations, all grown under the same conditions. We selected two materials with strong (LC19) and weak (LC2) rhizome growth abilities from nine materials and treated them with exogenous melatonin. We found there were significant positive correlations between stem length, plant height, leaf number and rhizome traits. Additionally, rhizome traits showed significant positive correlations with photosynthetic indices and chlorophyll content. Specifically, for LC2, treatment with 200 μmol/L melatonin significantly increased root length, the number of extravaginal ramets and rhizome clonal growth rate by 88.72%, 43.75% and 43.70%, respectively, resulting in significant increases in aboveground traits. Similarly, for LC19, 200 μmol/L melatonin treatment led to significant increases of 74.66%, 23.02%, 62.71% and 62.72% in four traits, respectively, along with aboveground trait improvements. Furthermore, around 300 μmol/L melatonin treatment promoted photosynthetic efficiency in LC2, while around 100 μmol/L melatonin treatment had the same effect in LC19. In conclusion, our study highlights the relationship between rhizome growth ability, aboveground growth and photosynthesis in Leymus chinensis. Additionally, it suggests that exogenous melatonin can enhance aboveground growth and photosynthesis by regulating rhizome growth.