Abstract: As one of the most important tributary in Liaohe River Basin, Taizi River Basin is a region of industrial and agricultural production base and energy base. Under the extensive economic development mode, Taizi River encounters serious water pollution and deteriorative aquatic ecosystem problem. To ensure ecosystem health and human sustainable development, the National Water Pollution Control and Management Technology Major Project has been implemented in Taizi River Basin since 2009. Periphyton, which usually grows on stone surface, is sensitive to a wide range of environmental variables, because its community structure could response quickly to physical, chemical and biological variations in the environment. To access the aquatic ecological condition of Taizi River Basin in recent years, the periphyton communities and aquatic environment factors at 44 sampling sites in 2009 and 2014 were investigated and analyzed, and the concentration limits of primary water environmental factors were also explored for the periphyton community protection. The results were as followed:(1) Compared with those in 2009, the integrity of periphyton community was improved, especially periphyton density, species richness and community diversity were significantly increased (P < 0.05) in 2014. Otherwise, there was a general increase in the relative abundances of the periphyton species with negative response to the adverse environmental disturbance in 2014, and the relative abundances of the periphyton species with positive response to the adverse environmental disturbance were generally decreased in community composition. (2) Compared with 2009, TDS, SS, TN and NO₃^--N concentrations were significantly improved (P < 0.05), and the concentration of DO was significantly decreased (P < 0.05) in 2014. By Canonical Correspondence Analysis, the total nitrogen and ammonia nitrogen were the primary environmental factors affecting periphyton assemblage structure in 2009, whereas the total dissolved suspended solids, TN and NH₄⁺-N were the dominant factors (P < 0.01) in 2014. (3) The results of LOWESS and independent sample t test indicated that P-IBI scores significantly changed when TDS concentration > 185.00 mg/L, TN concentration > 1.00 mg/L and NH₄⁺-N concentration > 0.22 mg/L. Concentration therefore, this study can provide data support for the aquatic ecological protection in Taizi River Basin and theoretical basis for water environment management in China.