Microwave modification of activated coke is reported as a green and simple route to improve its synergistic desulfurization and denitrification. The results showed that microwave irradiation improved the specific surface area and pore volume, decreased the pore size, and activated the surface functional groups of the activated coke. Under the conditions of a microwave power of 500 W and a modification time of 30 min, the specific surface area was increased from 185.9 m2/g to 351.7 m2/g, the pore volume increased from 0.042 m3/g to 0.111 m3/g, and the characteristic peak strengths of C=C and -OH drastically increased. When the reaction temperature was 140 °C and the O2 concentration was 10% (by volume), the desulfurization and denitrification efficiency were maintained at levels greater than 90% and 80% for 30 min and 15 min, respectively. The C-O content increased, and the C=C and -OH content decreased after undergoing desulfurization and denitrification. The desulfurization and denitrification products were primarily sulfate and nitrate. This provides theoretical support for the application of microwave modified active coke in low temperature desulfurization and denitrification.