The water samples from Lake Poyang were collected in January(dry season) and July(wet season) of 2014 in order to measure the corresponding physical factors, chlorophyll-a concentration and photosynthetically active radiation. Vertically Generalized Production Model was used to estimate the primary productivity of phytoplankton, characteristics and relationship with the lake environmental factors. Results show that the range of phytoplankton's primary productivity in Lake Poyang is fluctuated between 83.50 and 355.43 mg C/(m³·d), and the average is 193.33 mg C/(m³·d) during the dry season. The spatial distribution of primary productivity is mainly affected by different types of water quality in dry season. The primary productivity is negatively correlated with nutrients, of which NH₄⁺-N was highly significant due to the absences of nutrient limitation. In wet season the range of primary productivity of phytoplankton is between 113.80 and 1134.06 mg C/(m³·d), and the average is 412.12 mg C/(m³·d), which was affected by the river flow inputs. Primary productivity was significantly positively correlated with the total phosphorus and suspended solids concentrations. Because the positive effect caused by suspended solids was greater than the negative effect on phytoplankton, these effects caused that the restricted phosphorus nutrients occur frequently. The overall average velocity is about 0.28 m/s in the Lake Poyang which is beneficial to the growth of phytoplankton. However, the average speed in the south is approximately 0.21 m/s, while it is approximately 0.35 m/s in the north. Therefore, eutrophication, or even algal bloom are more often occurred in the southern Lake Poyang.