Submerged macrophytes are critical component in ecological restoration of lakes, which harbor epiphytic microbes that play important roles in nutrient cycling and water quality improvement in aquatic ecosystems. However, the responses of planktonic and epiphytic microbial communities to different restoration strategies, as well as the underlying mechanisms, remain largely unknown. To address this gap, we investigated bacterial and microeukaryotic communities in both water column and phyllosphere of Vallisneria natans (V. natans) across three areas of the urban Lake Xuanwu: a near-natural restoration (NR) area, an enclosure restoration (ER) area, and an unrestored (UR) area, to uncover how ecological restoration shapes microbial communities and their potential functions. The results showed that the NR area exhibited higher coverage and greater species richness of submerged macrophytes, along with lower concentrations of total nitrogen (TN), total phosphorus (TP), turbidity (Turb), and chlorophyll a (Chl a). The diversity of both planktonic and phyllosphere microbial communities was significantly higher in the NR area than in the ER and UR areas. The dominant microbial taxa in the phyllosphere of V. natans differed from those in the surrounding water, with obvious compositional differences among the three restoration areas. Variations in microbial community structure were primarily driven by differences in TN, TP, Turb, and Chl a, with bacterial communities being more strongly influenced by environmental factors than microeukaryotic communities. Functional bacterial groups involved in nitrification and nitrate ammonification were selectively enriched in the phyllosphere of V. natans, and the abundance of nitrogen-cycling populations was significantly correlated with ambient nitrogen concentrations in the water. The microbial co-occurrence networks in the NR area displayed greater complexity and stability than those in the ER and UR areas. Compared with the microeukaryotic network, the bacterial network contained more nodes and edges connecting nodes with environmental factors, reflecting a stronger susceptible to environmental influence for the bacterial community. Moreover, based on functional predictions, the key bacterial genera within the phyllosphere network of Vallisneria natans may play important roles in carbon and nitrogen cycling. This study elucidates the mechanisms by which submerged macrophytes regulate microbial community structure, interaction networks, and keystone functional taxa during ecological restoration to improve water quality, thereby providing scientific support for the ecological restoration of eutrophic lakes.