The temporal and spatial variations in the Normalized Difference Vegetation Index (NDVI) were analyzed and the factors that affect the growth condition of different types of vegetation in Lake Taihu were identified using MODIS NDVI data gathered from 2000 to 2015. MOD13Q1 data were obtained with 16-day temporal resolution and 250 m spatial resolution. Projection transformation and irregular cutting were implemented according to the vector diagram of Lake Taihu. Then, abnormal values were eliminated by the band math module of ENVI 4.7 software (The range of NDVI is between -0.2 and 1). We analyzed the corresponding NDVI values and imported the results to MATLAB R2015b software according to the latitude and longitude that determine corresponding pixel points. The result indicated seasonal and inter-annual variations in the NDVI of aquatic vegetation in Lake Taihu. Annual minimum NDVI occurred in winter, and the maximum in August or September, reaching 0.35 with flourishing vegetation growth. The multi-year mean NDVI was 0.1, and the annual mean NDVI was the largest in 2007 at 0.14. The spatial distribution of NDVI and the different types of vegetation can be distinguished in Lake Taihu. The northwestern area of the lake (Zhushan Bay and Meiliang Bay) was covered by planktonic algae; the maximum value was larger than 0.2 in this area. The east area was mainly covered by submerged vegetation; the maximum value exceeded 0.6 in this region. In the different ecological areas of Lake Taihu, the responses of vegetation growth to meteorological factors differed. The seasonal NDVI variation of Lake Taihu was of single-peak type. The growth season of aquatic vegetation was from April to November. The inter-annual variability of spatial distribution of NDVI in the planktonic algae area could reflect the dynamics of cyanobacteria distribution. Submerged vegetation growth was positively correlated with mean air temperature. However, wind speed affected the growth of the planktonic algae.