Promoting biomass utilization, the objectives of this study were to clarify the spatial distribution of nitrogen, one of the most important fertilizer components in the methane fermentation digested slurry (i.e., the digested slurry), and to establish an effective method to apply spatial-uniformly digested slurry with irrigation water in the rice paddy field. A numerical model describing the unsteady two-dimensional flow and solution transport of paddy irrigation water was introduced. The accuracy of this model was verified with a field observation. The tendencies of the TN simulated in inlet and outlet portions had good agreement with the measured data and the accuracy of the numerical model could be verified. Using the numerical model, scenario analyses were conducted to determine the method for spatial-uniform application of the digested slurry with irrigation water. The simulated results indicated that drainage of the surface water and trenches at the soil surface were effective for spatial-uniform application of the digested slurry with irrigation water in the rice paddy fields. The effect of the trenches was maximized when the surface water of the rice paddy field was drained adequately.