The aim of this study was to simulate microwave heating characteristics to investigate the lipid quality in rainbow trout, including the impact of the heating rate, maximum temperature, and thermal processing level on the extent of lipid oxidation and on the fatty acid extraction coefficient. Increasing F0 from 3 to 6 min improved fatty acid retention at high heating rates but led to a decrease in the measured results at low heating rates. Elevated thermal processing levels and maximum temperatures were observed to intensify the oxidation. At F0 = 3 min, an increase in maximum temperature led to an increase in the total lipid extraction coefficient but a decrease in the fatty acid extraction coefficient. However, an increase in maximum temperature resulted in a decrease in both extraction coefficients when F0 was 6 min. The coefficient spectra of fatty acid extraction obtained from the microwave and traditional heat treatments showed nonparallel trends, confirming the presence of non-thermal effects during microwave thermal processing. In conclusion, compared to conventional heat treatment methods, microwave processing has significant potential for enhancing the lipid quality of ready-to-eat rainbow trout products and effectively reducing production costs.