<p>Taihu lake is a typical eutrophic lake, which has experienced severe degradation in recent decades, understanding the spatio-temporal variation of ecological health can assist guide lake management in the future. Here, benthic macroinvertebrate compositions, in addition to waters and sediments, were collected from Taihu lake at 16 sampling sites and used to evaluate spatio-temporal variation in benthic macroinvertebrates. Further, a benthic index of biotic integrity (B-IBI) was developed to assess lake ecological health. Significant spatial heterogeneity in benthic community composition was observed (<i>p</i> &lt; 0.01): eastern areas exhibited higher biodiversity (H’ = 1.63 ± 0.59) than northern areas (H’ = 1.18 ± 0.51) (<i>p</i> &lt; 0.05), with the highest mollusk abundances and lowest arthropod proportions. The B-IBI assessment results indicated an overall “good” level of ecological health. Specifically, the eastern area was rated “healthy”, while the northern area showed the poorest ecological health condition when compared with other areas. Temporally, healthy sites reached the lowest proportion in August, while western and southern areas showed significant long-term deterioration (<i>p</i> &lt; 0.05). Variation in benthic community composition was closely associated with environmental and ecological changes, and especially mollusk abundances were positively correlated with water total nitrogen (TN_w). This study provides empirical evidence for zonal management strategies (e.g., prioritizing northern area restoration), highlights TN_w control as a key intervention for lake health, and offers transferable insights for the sustainable management of eutrophic freshwater ecosystems.</p>