Abstract: The ecosystem health of the upstream section of Liaohe River was evaluated by benthic index of biotic integrity (B-IBI) combined with unmanned aerial vehicle (UAV) remote sensing. From the spatial distance, the selection scientificity of reference sites was verified by analyzing the landscape pattern through the buffer. Further study of the ecological processes of the reference sites was conducted. Based on the physical, chemical, land utilization information, UAV remote sensing orthophoto maps and water quality parameters of 16 habitat sampling sites in the main upstream area, four reference sites were screened out. Analysis of the range of index value distribution, Pearson correlation and judgment ability were performed on 32 candidate metrics, while six core indexes were selected and normalized. The criteria for benthic macro-invertebrates in the upstream of Liaohe River were determined to be healthy (B-IBI > 3.90,0.82% of the area), sub-healthy (2.93-3.90,1.26% of the area), fair (1.95-2.93,3.43% of the river, poor (0.98-1.95,3.57% of the area), and very poor (0-0.98,0.92% of the area). The relationship between B-IBI and habitat quality was remarkably correlated (R²=0.55, P<0.01). In general, the structure of macro-invertebrates in the main stream of Liaohe upstream mainly consisted of species indicating moderately polluted water.