River crab meat samples were preserved with high power pulse microwave (HPPM) and eugenol. The total viable counts (TVC) and total volatile base nitrogen (TVB-N) contents were determined during 5-day storage. The microbial diversity of samples treated with different preservation methods was analyzed by high-throughput sequencing. Results showed that HPPM combined with eugenol could significantly delay the increase of TVC and TVB-N contents during storage. The dominant spoilage bacteria in crab meat samples was Bacillus. Addition of 2 μL/g eugenol and treating with HPPM at 900 kW， 200 Hz for 5 min had a strong inhibitory effect on the growth of Bacillus.