Excessive proliferation of filamentous green algae (FGA) is a problem that commonly occurs following the remediation of submerged macrophytes during lake restoration. Cultivation of submerged macrophytes changes the physical and chemical environment and micro-habitats for survival and growth of FGA. However, effects of submerged macrophytes on FGA and the mechanisms are largely unknown. In this study, artificial grass (controls) and two submerged macrophytes (Potamogeton maackianus and Vallisneria natans) with different leaf complexity were cultivated at densities of 3, 6, and 9 in aquaria for a month. The proliferation of FGA, photosynthetic performance of macrophytes, and possible roles of bacteria in the interaction of macrophytes and FGA were studied. Compared with controls, planting of P. maackianus promoted the proliferation of epiphytic FGA, and the effects were density-dependent. Also, density-dependent decrease of photosynthetic performance of P. maackianus were observed. However, in the groups of V. natans, proliferation of epiphytic FGA showed density-dependent inhibition, but photosynthesis of V. natans showed density-dependent promotion. Furthermore, photosynthesis of macrophytes was negatively correlated with growth of epiphytic FGA (Chl a contents). Abundances of epiphytic bacteria taxa such as members of orders Rhodobacterales, Nitrosomonadales and Gemmatimonadales on P. maackianus were greater than those on V. natans. The abundances of these bacteria were positively related to Chl a contents of epiphytic algae (FGA). Thus, proliferation of FGA might be partly attributed to accumulation of certain bacteria taxa on the submerged macrophytes planted during lake restoration. To avoid excess proliferation of FGA, careful selection of submerged aquatic macrophytes is needed.