The most common natural disturbances in shallow lakes are wind-induced waves, which cause catastrophic changes in the aquatic fauna of lakes. Recovery from these changes is always prolonged. The objective of this study was to understand the resilience and recovery of the particle-attached bacterial community composition (PABCC) after frequent wind-wave disturbance in a large shallow eutrophic lake. To accomplish this, we designed a mesocosm experiment including an undisturbed control, and a physically disturbed treatment that stimulated the superposition of two different intensities of wind-induced waves in the large shallow eutrophic Lake Taihu, China. The PABCC was determined by denaturing gradient gel electrophoresis, following by cloning and sequencing of the selected samples. We observed that the most marked change of the PABCC occurred in the disturbed treatment, in which the concentrations of suspended solids (SS) and the water turbidity varied strongly. However, we observed low recovery of the PABCC within 4 days post-disturbance when the investigated environmental factors had also recovered. Our results indicated that the resistance of the PABCC is low, and resilience is also low following frequent disturbance by wind-waves in a large shallow eutrophic lake.