The effect of microwave (MW) pre-treatment on the extraction of flaxseed oil was investigated by hot extraction (HE). Nine MW pre-treatments were established, combining three MW radiation intensities (12, 18 and 24 W/g) and three MW radiation times of pre-treatment (90, 150 and 210 s). Extraction yield increased significantly with MW pre-treatments of flaxseed, and a max oil extraction yield (78.11%) can be obtained using MW pre-treatment at 18 W/g for 210 s. Scanning electronic microscopy showed that the microstructure of treated samples (18 W/g and 210 s) was modified compared with that of untreated samples. The fatty acid compositions (palmitic acid 5.85±0.01%, stearic acid 3.00±0.01%, oleic acid 17.64±0.07%, linoleic acid 16.16±0.06%, and linolenic acid 57.37±1.32%) of the oils extracted by the MW pre-treatments HE were similar with that of the conventional HE method. Results showed that fatty acid compositions of flaxseed oil were not affected by MW pre-treatments.