The purpose of this study is identify chemical changes in yield components of soil using organic fertilizer for cultivating rice and establish reasonable methods of fertilization. In chemical change, comparing the control plot, the soil using organic fertilizer consistently for three years for cultivating rice showed an increase in pH and available phosphate in the experiment plots provided by the organic fertilizer, increase in spikelet number and 1000 grain weight in terms of yield components, and increase in yield in the three-year experiment plots. As for the quality of brown rice, the rate of head rice showed no difference when compared to that of the control plots. As for protein content, it was difficult to identify a statistical significance between the control plots and the experiment plots in 2009, but since 2010, the protein content of the experiment plots has been lower than that of the control plot, indicating that fertilization of organic fertilizer was effective in terms of rice quality. In conclusion, long-term use of organic fertilizer improved the chemical properties of soil and increased yield when compared to practical fertilization. Reasonable fertilization was identified to fertilize the nitrogen component of organic fertilizer to be a level of 12kg/10a.