In order to explore the vertical distribution characteristics of microcystin (MC-LR, MC-RR, MC-YR) concentration in the water body and sediment of Meiliang Bay, surface water, overlying water, mixed water, interstitial water and columnar sediment samples at six points were collected in May 2018, and the microcystin concentrations were analyzed by ultra-high performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS). The results indicated that the MC-LR, MC-RR, MC-YR concentrations in water (surface water, overlying water, mixed water and interstitial water) ranged from 11.80-1297.14, 2.50-818.40, 1.80-176.00 ng/L, respectively. The MC-LR concentration in surface water, overlying water and mixed water were higher than MC-RR and MC-YR concentrations, but there were no significant difference between MC-RR and MC-YR concentration. The order of MC concentrations isomer in interstitial water was:MC-LR > MC-RR > MC-YR. The MC concentrations isomer (MC-LR, MC-RR, MC-YR) in interstitial water were all far higher than those in surface water, overlying water and mixed water in vertical profiles of water, the MC isomer concentrations in surface water were slightly higher than those in overlying water. The MC isomer concentrations in mixed water were between surface water and overlying water. The MC-LR, MC-RR and MC-YR contents in sediment with a depth of 10 cm ranged from 0.60-26.95, 0-0.90 and 0-8.10 ng/g, respectively, and the order of the average content of three MC isomers in the 1-10 cm layer was MC-LR > MC-YR > MC-RR. The detection rates of MC-LR, MC-RR and MC-YR were 100%, 70% and 92%, respectively. In the vertical distribution of sediment, the MC-RR concentration was low and showed little change, the overall trend of MC-YR and MC-LR contents increased first and then decreased with the increasing of the sediment depth. The results of correlation analysis indicated that MC isomer concentrations in surface water and mixed water were positively correlated with total phosphorus (TP) concentration, respectively, but did not show correlation with total nitrogen (TN) concentration. The MC concentrations in overlying water, interstitial water and sediment were positively correlated with TN and TP concentrations, respectively.