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Outbreaks of periphytic algae, including filamentous algae, have been observed after submerged macrophyte restoration and are common in early stages. Dynamic changes in the periphytic algae community on <i>Vallisneria natans</i> and artificial <i>V. natans</i> were investigated in situ, and their characteristics were compared on the two substrates. The results showed that more periphytic algae species occurred on <i>V. natans</i> (77 taxa) than on artificial <i>V. natans</i> (66 taxa) (F = 2.089, <i>p</i> = 0.047). The cell density and chlorophyll a (Chl. a) content of periphytic algae were 3.42–202.62-fold and 2.07–15.50-fold higher on the artificial substrate than on <i>V. natans</i>, respectively. Except for <i>Lyngbya perelagans</i> (i.e., the only common dominant periphytic algae species on the two substrates), the dominant species on <i>V. natans</i> were <i>Cocconeis placentula</i> and <i>Ulothrix tenerrima</i>, while those on the artificial substrate were <i>Stigeoclonium aestrivale</i>, <i>Oscillatoria tenuis</i> and <i>Achnanthes minutissima</i>. The cell density of periphytic algae was significantly affected by the total phosphorus (TP) and NO₃⁻-N and electric conductivity on <i>V. natans</i>, and by TP and NH₄⁺-N on artificial <i>V. natans</i>. The malondialdehyde content of <i>V. natans</i> was significantly correlated with the periphytic algae biomass. <i>V. natans</i> was more affected by periphytic algae during its slow-growing period, and the contribution order of stress to <i>V. natans</i> was diatoms > cyanobacteria > green algae. Our findings might contribute to the understanding the effect of substrate specificity on periphytic algae communities, and have important implications for the restoration of submerged plants in eutrophic lakes.