In order to study the response characteristics of surface current to the changing wind field and the effect of wind field and surface current on the cyanobacteria migration in the Lake Taihu, systematic field observation was carried out. In this study, the surface current was observed by the GPS particle tracers, while the characteristics of surface current and the accumulation process of cyanobacteria blooms in the Lake Taihu under varying wind condition were analyzed by combining the variation characteristics of wind field and remote sensing map. The results show that the wind is the main driving force of surface current in the Lake Taihu. However, due to the influence of topographic characteristics, shoreline characteristics and et al, the response of surface current to the wind field in different water areas is not completely consistent. The surface currents of the Lake Taihu under the influence of wind field have wide spatial differences, which is the dominant factor leading to different concentrations of cyanobacteria in different areas during the migration process, and this phenomenon is one of the important reasons for the regional cyanobacteria bloom. The process of wind field, surface current and cyanobacteria migration and aggregation are a response system of successive conduction. The current field under the influence of suitable wind field is an important external factor to promote the large area of cyanobacteria blooms in a short time.