[Objective] Periphyton is ubiquitously distributed in paddy fields, directly affecting nutrient cycles and their bio-availabilities. However, no study regarding effects of periphyton on rice growth has been reported.[Method] In this study, model paddy ecosystems with three types of soils were simulated under controlled conditions to investigate the effects of periphyton on rice seed germination and seedling growth.[Result] Results show that periphyton of three types of soils was mainly composed of Proteobacteria, Cyanobacteria and Bacteroidetes, while the diversity of periphyton of the three soils was significantly different, and that grown in soil from Yanbian (YBP) had the highest OTU number and Chao1 index. Furthermore, there were significant differences in carbon metabolic activity among the three periphyton (P<0.05). The Pearson correlations indicated that periphyton composition and diversity was positively correlated with soil pH, TP, TOC and Mn contents (P<0.05). The carbon metabolism activity of YBP was the highest during the whole growth period, while that of soil from Yingtan (YTP) was the lowest. The presence of periphyton greatly increased the germination index of rice seed (by maximally 18%), and α-amylase activity in the presence of periphyton was increased significantly (P<0.05). Besides, the periphyton covering on paddy soil surface from Yanbian (YBP) significantly promote shoot length and its biomass (P<0.05). The Pearson correlations indicated that seed germination and survival rate was positively correlated with periphyton chemical properties.[Conclusion] To summarize, this study indicates that the presence of periohyton biofilm during seed germination period was propitious for rice growth. Results of this study provided an insight into understanding the periphyton-plant relationships with different soil-types and also new approaches to controlling plant phenology by regulating the growth of periphyton.