Periphyton is widely distributed in paddy fields and its interactions with paddy soil and rice growth have been reported rarely. In this study, model paddy ecosystems with different additional soil substrates were simulated under controlled conditions to investigate the effects of periphyton on rice seed germination and seedling growth. Results show that the selected soil substrates had significant effects on the metabolic activities and growth of periphyton in paddy fields. The addition of straw to soil enhances but the addition of biochar leads to attenuation of periphyton growth. The presence of periphyton in the paddy system, especially with straw in soil greatly increased the germination index of rice seed (by maximally 21%). However, the biochar treatment in the presence of periphyton was detrimental for the seed vitality with a decrease of 30%. As a result, the periphyton cover on paddy soil surface significantly inhibited the growth of rice seedling, including rice height, leaf width and biomass. To summarize, this study indicates that the presence of periphyton during seed germination period was detrimental for rice growth, but could be used to control the weed growth. Thus, this study provided insight into understanding the periphyton-plant relationships with different soil-substrates and also new approaches to controlling weeds in paddy fields by regulating the growth of periphyton.