Trait-based approaches have been widely used to explore the relationships between submerged macrophytes and their surrounding environments. However, the effects of functional traits on ecological functions of submerged macrophytes in eutrophic lakes are still not well understood. Here, 1745 individuals of eight dominant submerged macrophyte species in 19 Yangtze floodplain lakes were collected and classified as needle-leaf (Myriophyllum spicatum, Ceratophyllum demersum, Stuckenia pectinatus, Najas minor) or flat-leaf (Vallisneria natans, Hydrilla verticillata, Potamogeton wrightii, Potamogeton maackianus) types according to photosynthetic trait-based cluster analysis. The flat-leaf type submerged macrophytes possessed greater photosynthetic (e.g. higher Fv/Fm) and morphological traits (e.g. higher SLA), while the needle-leaf types held greater stoichiometric traits (e.g. higher plant N/P). Moreover, the RDA analysis indicated that water depth (distribution depth of submerged macrophytes) was the key factor influencing functional traits of flat-leaf types, while it was water quality (e.g. WTP and WChl a) for the needle-leaf types. Furthermore, the flat-leaf types showed better performance in improving underwater light conditions (e.g. SD, Kd, Zeu/WD and Red/Blue) and water quality (e.g. WChl a and TSM). Additionally, distribution depth (WD) of the flat-leaf types was shallower than the needle-leaf types in eutrophic shallow lakes along the middle-lower reaches of the Yangtze River. Our study highlights that functional traits of submerged macrophytes in eutrophic shallow lakes affect their ecological functions.