In order to study the purification effect on the particle size of matrix in ecological filter bed, four ecological filter bed units with different particle sizes (0~2mm, 2~15mm, 15~30mm, 30~50mm) are designed to purify the polluted river water. Results show that the particle size of matrix has considerable influence on the polluted river water quality improvement, and the purification effect decreases gradually as the particle size of matrix increases. During the whole experimental period, the ecological filter bed unit with the particle size of 0~2mm is the best in all four systems, and the average removal of it is 62.77% for CODCr, 73.04% for TN and 67.40% for TP respectively.