The benthic index of biotic integrity (B-IBI) is an ecological method that widely used in river health assessment, but very few studies focus on the adaptability of B-IBI in river health assessment on the time scale. This study investigated the community structure of benthic macroinvertebrates systematically in the Ili River in May, July, August and October of 2013-2015. Meanwhile, we evaluated the temporal pattern on the results of health assessment for the Ili River based on the B-IBI. The results of non-metric multidimensional scaling (NMDS) showed that the community structure of benthic macroinvertebrates in different months in the Ili River revealed a high similarity. We sifted a total of 30 candidate metrics, which belong to 6 categories, including community richness, the proportion of individual species, functional feeding group, pollution tolerance, habitat quality and biodiversity index. Ultimately, the number of Ephemeroptera, Plecoptera, Trichoptera (EPT) taxa, the percentage of Ephemeroptera, the percentage of tolerant groups, Biotic Index (BI) and the percentage of clingers were selected as the key metrics of the B-IBI health assessment system in the Ili River. The assessment grades of B-IBI were as follows:B-IBI>3.38 representing healthy, 2.53P>0.05), suggesting that the overall health status of the Ili River was not significantly affected by seasonal changes. There was a significant difference between the B-IBI in 2013 and that in 2015 (P<0.05). The health status of Ili River has a trend of getting better year by year. The biological health assessment of the river needs long-term and systematic investigation and research to reflect the health status of the river. The non-parametric tests indicated that, overall, the B-IBI scores of the reference sites were significantly higher than those of the impaired sites, which indicated the adaptability of the B-IBI health assessment system in the Ili River. This study can provide theoretical guidance for the river health evaluation based on the B-IBI in times of time scale.