Eutrophication and phytoplankton blooms threaten the water quality of many reservoirs, especially deep ones. Periphyton is an important component of aquatic ecosystems that can compete with phytoplankton for light and nutrients. However, studies on the dynamics of periphyton development in deep reservoirs are rare. Here, the growth characteristics of periphyton on the artificial substrate (AS) in both open water and enclosures of the Three Gorges Reservoir (TGR) are investigated. The development and relative importance of periphyton are analyzed. The results indicate that mass growth of periphyton is observed on the AS platforms after several weeks. A potential phosphorus limitation for periphyton development in the TGR is evidenced by the relatively high TN/TP ratio in the water column. The differences of phytoplankton biomass in two enclosures suggest the existence of interactions between phytoplankton and periphyton. The results indicate that the artificially loaded AS on the water surface of the deep reservoir leads to the redistribution of nutrients and light between phytoplankton and periphyton. The results are very encouraging because the use of AS for periphyton incubation is an economical and practical way to reduce the probability of phytoplankton blooms in deep reservoirs, especially when the nutrient loads cannot be reduced effectively in a short period.