The need for a rapid, sensitive, and reliable analytical method for microcystin-LR has been emphasized by the awareness of toxic cyanobacteria as a human-health risk through drinking water. Microcystin-LR is the most commonly reported microcystin which is produced by cyanobacteria. The WHO guideline for microcystin-LR in drinking water is 1mug/l. In this paper, an effective method has been developed by application of high-performance liquid chromatography/tandem electrospray ionization mass detector in the determination of microcystin-LR in surface water sample. At the LC-MS-MS CID-full scan mode, different relative collision energies have been tested with 30% being used for further microcystin-LR analysis. The possible mass dissociation path has been proposed. Based on 30% relative collision energy, present method has an excellent method detection limit (MDL), which is as low as 2.6ng/l. To the best of our knowledge, this represents one of the most sensitive methods in existence for the microcystin-LR analysis. This method has also been validated by evaluation of the calibration linearity, precision, accuracy, recovery, and mass ratio stability.