Based on the investigation of the hydrology, water quality, periphytic algae, and habitat conditions of 20 hydrologic sections in the Tieling, Shenyang, and Panjin reaches of Liaohe River from June to August 2009, the indicators and their weights for the health assessment of aquatic ecosystem in the River were screened and determined by the method of principal component analysis, and the River's health assessment indicator system and health assessment standard system were constructed. The modified gray correlative degree method was also used to evaluate the aquatic ecosystem health condition at six sections of the River. Among the sections evaluated, three of them had a fair health level, two were worse or worst, and only one reached sub-health degree, suggesting that the aquatic ecosystem in the River was seriously degraded. Special attention should be paid to the ecological recovery of the river system, and comprehensive measures should be taken to control the River' s water pollution.