Community structure of macrozoobenthos and the bioassessment on water quality in a second order river—Hujiaxi Stream of Qingjiang River basin were investigated from April 2006 to March 2007. The results showed that, among collected altogether 87 species of macroinvertebrates, there were 3 species of Annelida, 3 species of Mollusca, 76 species of aquatic insects, and 5 species of Malacostraca. The community structure exhibited obvious spatial and temporal variations. The species number reached its peak in June, and descended to the lowest in December. There was the largest species number in Site 5, and more species macroinvertebrates were presented in June than those in other months. Over 75% of the collected species could inhabit in all six types of microhabitats. The density of the community reached its peak in April at 3293 each/m², while biomass attained its peak in December at 163 g/m². The water quality was bio-assessed with Shannon-Weaner diversity, Biotic Index (BI) and Family Biotic Index (FBI), and results showed that the river water was fairly clean during the sampling period. Considering the coincidence with physical-chemical parameters, BI and FBI bio-assessment methods were much fit to apply in rivers of China.