The comprehensive assessment of environmental quality is useful for comparison of environmental quality and identification of pollution trends. In the comprehensive assessment methods, many studies proved that grey clustering method is accurate and effective. However, the zero-weight problem occurs in the traditional grey clustering method (TGCM). This flaw may lead to the assessment result distortion. To solve this problem, this paper proposes a modified grey clustering method (MGCM) in which the linear whitening functions in the traditional grey clustering method is replaced by exponential functions. The modified method was applied to assess water quality of four monitoring sections in the Yuhang section of the Tiaoxi River. Then, the results were compared with those obtained with the TGCM. The comparisons show that solving the zero-weight problem can lead to different assessment results and the MGCM is effective to solve the zero-weight problem. The MGCM is more accurate than the TGCM.