Microwave sterilization is a novel potential sterilization technology to improve food quality. An industrial microwave sterilization system was used to sterilize imitation crab meat under thermal processing intensity F0 = 1, 2, 3. The characteristics of the microwave process, such as heating rate, processing time, and C100, were calculated. In addition, the quality of processed imitation crab meat was investigated. Compared with the conventional retort method, microwave sterilization significantly shortened the processing time of imitation crab meat by 63.71% to 72.45%. Under the same thermal processing intensity, microwave sterilization has demonstrated better results than retort sterilization in terms of water-holding capacity, color, and texture. Furthermore, microwave-treated imitation crab meat ingredients had a greater capacity to bind water molecules and obtained a more appropriate secondary protein structure. In addition, microwave technology can better preserve the unsaturated fatty acids (UFA) of imitation crab meat, which are 9.14%, 1.19%, and 0.32% higher than the traditional method at F0 = 1, 2, 3. The results would provide useful data for the subsequent research and development of ready-to-eat surimi products.