In this paper, hydride generation-atom fluorescence spectrometry method was used to analyze arsenic and mercury in water. A series of analytical conditions were studied, including lamp current, height of atomic part, gas flow, interference ions, acidic medium and acidity. The results show that the two channels HG-AFS determination of arsenic mercury has the advantages of simple, rapid, less noise and high sensitivity. The determination limits of arsenic and mercury had been proved to be 0.07 μg·L^-1 and 0.009μg·L^-1, and the linear ranges to be(0-80.0)μg·L^-1 and(0-8.00)μg·L^-1 under optimum conditions.