The microwave digestion system was equipped with oxygen bomb. The coal sample was treated using microwave induced oxygen bomb combustion. The content of fluorine and chlorine was determined by ion chromatography. The pretreatment conditions were listed as below: the oxygen bomb reflux time was 30 min, the absorption solution was 50 mmol/L ammonium carbonate, and 15% quartz sand was added. It was found that the recovery of fluorine could be greatly improved, while the absorption of chlorine was not affected. The mixed leaching solution of sodium carbonate and sodium bicarbonate with flow rate of 1.00 mL/min was selected for the ion chromatography. The detection limit of fluorine and chlorine was 0.010 mg/L and 0.011 mg/L, respectively. The mass concentration of fluorine and chlorine in range of 0.05-50 mg/L was linear to the peak area. The correlation coefficients of calibration curves were higher than 0.999. The proposed method was applied for the analysis of standard sample and actual sample of coal. The found results of standard sample were consistent with the certified values. The relative standard deviation (RSD) was less than 5%. The determination results of actual sample could also meet the requirements of relevant standards.