| Poyang Lake is the largest freshwater lake in China and an important drinking water source for Jiangxi Province. Since the year 2000, toxic cyanobacteria have been observed frequently in Poyang Lake. In this study, water samples were collected in the lake quarterly (April 2012, August 2012, October 2012, and January 2013) to examine the spatial and seasonal variations in the concentrations of microcystins (MCs; MC-RR, -YR, and -LR) and their relationships with physiochemical and biological factors. MCs were determined by ultra-high-performance liquid chromatography-electrospray ionization tandem triple quadrupole/mass spectrometry (UPLC-MS/MS). MC-RR (accounting for 75.01% and 71.34% of intracellular MC (IMC) and extracellular MC (EMC) concentrations, respectively) was the most dominant variant in Poyang Lake, followed by MC-LR (accounting for 21.95% and 24.97% of IMC and EMC concentrations, respectively), while MC-YR was detected in low concentrations (accounting for 3.01% and 3.69% of IMC and EMC concentrations, respectively). Total MC concentrations (IMC + EMC, TMC) ranged from 0.49 to 3517.85 ng·L-1, with an average of 337.43 ng·L-1 and only 2.53% (2 out of 79 water samples) of the water samples contained MCs concentrations exceeding the drinking water guideline level of 1 ng·L-1 for MC-LR proposed by World Health Organization (WHO). IMC concentrations showed significant relationships with Microcystis biomass (r=0.47, P<0.01), Oscillatoria biomass (r=0.68, P<0.01), Cyanobacteria biomass (r=0.56, P<0.01), and Chl-a (r=0.28, P<0.01), but no significant correlation was found between intracellular MC concentration and Anabena biomass (P>0.05), suggesting that Microcystis and Oscillatoria might be the main MCs-producing cyanobacteria in Poyang Lake. In addition, IMC concentrations were positively correlated with water temperature (r=0.51, P<0.01), transparence (r=0.69, P<0.01), Fe (r=0.43, P<0.01), and Zn contents (r=0.43, P<0.01), and negatively correlated with TN (r=-0.44, P<0.01), TP (r=-0.29, P<0.01), NH4+-N (r=-0.33, P<0.05), NO2--N (r=-0.28, P<0.05), Ca (r=-0.34, P<0.01), and Mg(r=-0.35, P<0.05), while no significant correlations were observed between IMC concentrations and pH, PO43--P, NO3--N, electrical conductivity, permanganate index, and Cu content (P>0.05). These results indicated that light intensity (represented by transparence), nitrogen, phosphorus, and water temperature might be the regulating factors of MCs production in Poyang Lake and trace elements (Fe, Zn, Ca, and Mg) can influence the MC production to a certain extent. IMCs and EMCs exhibited similar seasonal variations in Poyang Lake. The highest values of IMCs (531.87 ng·L-1) and EMCs (232.44 ng·L-1) were observed in summer. The concentrations of IMCs and EMCs in autumn were 31.97 ng·L-1 and 6.49 ng·L-1, respectively. Low concentrations were observed in spring (0.55 ng·L-1 and 0.88 ng·L-1 of IMCs and EMCs, respectively) and winter (0.69 ng·L-1 and 4.14 ng·L-1 of IMCs and EMCs, respectively). The highest IMCs and EMCs values of Poyang Lake in summer were 2298.08 ng·L-1 and 1219.77 ng·L-1, respectively, and the lowest values were 92.53 ng·L-1 and 38.80 ng·L-1, respectively. Overall, the concentrations of IMCs in eastern bays, the vicinity of Songmen Mountain, Banghu Lake, and its outlet were higher than those in other regions. However, the spatial distributions of EMCs in Poyang Lake were different from those of IMCs. EMCs concentrations in the vicinity of Songmen Mountain, Banghu Lake, and its outlet were higher than those in other regions.