A facile method based on liquid chromatography coupled with electrospray ionization tandem triple quadrupole mass spectrometry working in selected reaction monitoring mode has been established to analyze toxins in the algae and water samples. Twelve types of toxins (anatoxin, cylindrospermopsin, dinophysistoxin‐1, nodularin, okadaic acid, microcystins) were efficiently separated under optimized liquid chromatography coupled with mass spectrometry conditions in the selected reaction monitoring mode. Correlation coefficients of the calibration curves, all felt in the range of 0.9958–0.9998, indicated good linearity. The detection limits of toxins in this method were all lower than 0.20 ng/mL and the quantification limits were in the range from 0.04 to 0.60 ng/mL. Except for anatoxin, cylindrospermopsin, and nodularin, the other toxins’ recoveries varied from 55.45 to 140.85%. And the relative standard deviations of interday and intraday precision were at 8.61% (n = 5). The high‐performance liquid chromatography (HPLC)/electrospray ionization (ESI)–mass spectrometery (MS) method was also successfully applied to analyze the algae and water samples. Owing to its exclusive selectivity and excellent sensitivity, the developed method is a tool for comprehensive analyses of the 12 types of toxins at nanogram levels.