The effect of environmental factors on the gross primary production of phytoplankton is a basis for understanding the cyanobacteria bloom. Hereinto, water temperature and light energy are the key physical factors affecting phytoplankton growth. Based on phytoplankton primary productivity, water temperature profile and nutrient concentration observed in Lake Taihu in the spring of 2015, we explored the effects of these environmental factors on the the algae gross primary production. Results showed that in spring, water temperature and light energy were the key factors affecting algae growth, but the effect of nutrient was relatively weak in deep layers. The light energy and water temperature jointly affected the gross primary production of phytoplankton in shallower layer. The production were inhibited by light energy in surface layer. The water temperature increase promoted the ability of algae for the acquisition and utilization of light, improved the threshold value of light limitation, and enhanced the effect of light limitation, and shallowed the photo-inhibition depth. Current study is helpful to determine the evolution direction of aquatic ecosystems under climate change, and to provide an approach for the aquatic ecosystems restoration.