Abstract: The present study investigated the community structure of epilithic algae and characteristics of environmental factors among 9 sample sites in Ruxi River, a tributary of the Three Gorges Reservoir. The health of freshwater ecosystem in the stream conditions of Ruxi River was assessed via Index of Biological Integrity (IBI). The results indicated that there were significant spatial and temporal differences in the epilithic algae community structure in Ruxi River and conductivity, dissolved oxygen, nitrate nitrogen and turbidity were the major environmental factors in Ruxi River. IBI result showed that the upstream area of Ruxi River were in excellent biological integrity, while the midstream and downstream area were in severe impairment. The biological integrity in dry season was preferable to the normal. Thus, the biological integrity in natural stream of Ruxi River showed a general level, suggesting that a sub-health aquatic ecosystem was found in Ruxi River.