Lake Taihu was chosen as it is a typical large shallow lake, and algal model was established. 40 parameters in water quality model of the lake were filtered by previous research and sampled with Latin hypercube sampling method, and regionalized sensitivity analysis method and generalized likelihood uncertainty estimation method applied for uncertainty and sensitivity analysis, respectively. The results show that only 7 parameters selected were sensitive, and algal growth was the most important factor between the growth, basic metabolism, predation and settlement of algae. The extinction coefficient of chlorophyll was the most sensitive parameters in the light limitation of algae growth, and suboptimal temperature effect coefficient for growth also turned to be sensitive in the temperature limitation. In addition, uncertainty distinguished in different areas and period, more attention should be paid on low concentration areas and periods of algal blooms.