Abstract: With the improvement of living standard, edible fungus has become one of the common vegetables on the table of common people. In recent years, the safety problems of edible fungi have been emerging, which has seriously affected the healthy development of edible mushroom industry. It has become an urgent need for all levels of detection departments to develop an efficient, rapid and accurate method for the detection of pollutants in the mushroom substrate. In this paper, through the use of atomic fluorescence spectrometry to determine arsenic and mercury in the edible mushroom matrix, it provides the necessary basis and conditions for the safety of edible fungi.