Various kinds of substances in water, including organic matter, silt, zoogloea, algae, microorganisms etc., often cumulate on the leaf and stem surface in submerged macrophytes. A micro-interface is therefore established which varies in its composition, structure and thickness according to the actual environmental properties. It induces specific heterogeneous oxidation-reduction condition and provides organic material for nitrogen-cycle bacteria thus plays an important role in micro-interfacial processes such as ammonification, denitrification and anammox. The composition of this micro-interface, its responses to micro-environmental changes and functions in regulating nitrogen cycling constitute the fundamental horizon for better understanding the feature of submerged macrophytes in water management and ecological regulation. The present paper summarizes the research advancements on leaf and stem micro-interface in submerged macrophytes and its effect on water nitrogen cycling. The substance composition and micro-environmental property of the micro-interface are identified and reviewed respectively. Perspectives on future research are raised. Because of the compositional complexity in the leaf and stem micro-interface, recent studies have been mainly focused on the characterization of biotic components for example alga and microbe in submerged macrophytes. Much less information is available concerning the function of a certain component, especially that of the abiotic matters and that their effects on the micro-environmental properties in this micro-interface. Thanks to the development of microelectrode technique, in situ measurement of micro-environmental factors in the leaf and stem micro-interface and their spatial and temporal changes becomes feasible recently. However, current studies are much centered on the non-eutrophicated freshwater in which the major proportional periphyton is considered as autotrophic and the photosynthesis-sourced oxygen is to be consumed by respiration processes. The actual condition in eutrophicated waters is characterized by the abundance of oxygen-depleting substances and their accumulation on the leaf and stem surface of submerged macrophytes greatly changes the environmental properties in the micro-interface. Reports on the fluctuation of such micro-environmental properties in eutrophicated waters are still largely missing. The modulation of aquatic nitrogen cycling, specifically the denitrification by microbes in the micro-interface of submerged macrophytes, is the key biogeochemical process in ecological remediation of eutrophicated waters with high level of nitrogen nutrition. It has been proven that the existence of periphytic layers on the leaf and stem of submerge macrophytes could facilitate the aquatic nitrification-denitrification processes. The denitrification efficiency is apparently intensive in certain conditions. Nevertheless, these studies are mainly upon individual submerged plant or at the level of community as maximum, and in most cases estimating the nitrogen modulation according to the overall level of aquatic inorganic nitrogen, rather than the actual substance composition and inner environmental factors of the micro-interface that directly alter the nitrogen transportation and transformation. To further elucidate the secrets of leaf and stem micro-interface, studies are needed on the spatial and temporal variations in substance composition, structural characteristics and oxic-anoxic micro-inhabitants. The modulation mechanism of this micro-interface on the biogeochemical cycling of nitrogen in eutrophicated waters are fundamentally required.