Copper, iron, zinc and manganese in flaxseed were determined by inductively coupled plasma mass spectrometry(ICP-MS). After digestion by microwave-assisted, Cu, Fe, Zn and Mn were analyzed by using Standard and KED modes．In the present study, testing effectiveness of the two modes was compared. On this base, valid determination mode was selected for each of the elements and uncertainty evaluations of the four microelements were explored. According to JJFl059-1999 (Evaluation and Expression of Uncertainty in Measurement), the main influence factors were analyzed one by one. Each of the uncertainties was calculated separately. It was showed that the results of Cu, Fe, Zn and Mn in flaxseed determined by ICP-MS method were satisfactory. At the same time, the results obtained in this work were considered to be valuable as a reference for the evaluation of uncertainty in measurement of Fe, Cu, Zn and Mn with ICP-MS.