Seven molecular species of microcystins were qualitatively and quantitatively analyzed by both high performance liquid chromatography-tandem mass spectrometry （LC-MS/MS） and direct injection analysis （DIA）. The advantages and disadvantages of these two methods in precision， sensitivity and economy were compared， which were further used for the detection of microcystins in Melanioides. For LC-MS/MS method， the Waters XSelect HSS T3 （2.1 mm × 150 mm， 3.5 μm） was used as separation column with mobile phase of acetonitrile（0.1% formic acid） and water （0.1% formic acid）. The MS was operated in electrospray ionization（ESI） and multiple reaction monitoring mode（MRM） with linear range of 0.9965~0.9993 and relative standard deviation of 3.6%~6.1%. The limit of detection and the limit of quantitation were less than 0.54 ng/mL and 1.81 ng/mL， respectively. The recovery ranged from 73.9% to 83.4%. For DIA method， the fragment m/z 135.2 was selected as the characteristic ion with DP 60 eV and CE 55 eV. After precursor ion scanning （PreIS）， the microcystin were mainly ionized as [M+2H]2+. The comparison results of these two methods showed that the performance of LC-MS/MS was better than that of DIA， while DIA was faster in detection speed， which only cost one min to complete the determination of seven molecular species of microcystins. Finally， a total of 60 samples was analyzed by the two methods. The results showed that the positive samples were 63.3%， and the main pollution species were Mc-RR and LR. The results suggested that when the number of samples to be tested was large， DIA should be used for initial screening. For the positive samples， LC-MS/MS should be used for the secondary testing， which could effectively reduce the detection time， column loss and solvent consumption， and improve the reliability of the results. This analysis strategy can be applied to fast analysis of microcystins in water， animal， and plant samples， determine the monitoring and sampling position and frequency， the alert value， and the prevention and control， etc. This study could provide scientific basis for related departments to improve and strengthen the monitoring and management of aquatic products. It also could ensure the food safety and the development of offshore aquaculture.