(1) Setting a matrix dam in the paddy field drainage ditch has been recognized as an effective method to lower the velocity of water discharged from a paddy field in the drainage ditch, which can improve the purification efficiency of the drainage ditch for nitrogen and phosphorus pollutants, but the specific placement and thickness of the matrix dam have not been supported due to the insufficient research results. (2) Three thicknesses of the matrix dam were set in three locations of the physical model of the drainage ditch. By measuring the flow rate and water level in different sections, the optimal layout location and thickness of the matrix dam were determined. (3) When the matrix dam was located in section 1-1, the flow rate from sections A-A to C1-C1 was reduced by 0.159 m/s; when the matrix dam was located in section 2-2, the flow rate was reduced by 0.331 m/s; when the matrix dam was located in section 3-3, the flow rate was reduced by 0.360 m/s. (4) We concluded that the optimal design position of the matrix dam was section 3-3, 9.2 m from the entrance of the water flume, and the optimal design thickness was 0.3 m.