The effects of returning organic materials, such as Chinese milk vetch, rice straw and commercial organic fertilizer, on soil nutrients in paddy fields were studied through a 12-year long-term positioning experiment from 2010 to 2021. The results show that application of organic materials can effectively increase the contents of nitrogen, phosphorus, potassium and organic matter in paddy soil. Compared with the single application of chemical fertilizer, Chinese milk vetch increases the content of soil alkali-hydrolyzable nitrogen by 6.97%, commercial organic fertilizer combined with chemical fertilizer increases the content of soil available phosphorus by 49.30%, rice straw increases the content of soil available potassium by 49.32%. Application of green manure, rice straw and commercial organic fertilizer increase the content of soil organic matter by 6.0% to 7.5%, and improve soil acidity but the difference is insignificant. There are significant differences in the increases of soil nutrients among different organic materials. Chinese milk vetch green manure has the strongest fixation ability of soil nitrogen, organic fertilizer and rice straw have the most significant increase in soil phosphorus and soil potassium, respectively. In conclusion, long-term application of organic materials is an effective measure to fertilize soil and contribute to the sustainable utilization of paddy soil.