Trans fatty acids (TFAs) are formed in refined linseed oil during the deodorization step. Effects of deodorization on TFA formation in vegetable oils have been intensively investigated. However, the role of refining process (degumming, neutralization, bleaching) before deodorization on TFA formation in the deodorization step remains unclear. In this study, TFA generation potential in linseed oils refined by different ways of degumming, neutralization, bleaching was evaluated, and changes in their quality indexes were also measured. Results showed that adequate refining could improve the quality of linseed oil, while inadequate neutralization or bleaching induced more TFA formation during the deodorization step, suggesting that pigments or free fatty acids in linseed oils might promote TFA formation. Meanwhile, spiked experiments, in which partly refined linseed oils were spiked with pigments or α-linolenic acid, confirmed that pigments or free fatty acids in linseed oils induced the isomerization of unsaturated fatty acids. This study demonstrated that TFA formation in refined linseed oils could be mitigated by optimizing refining processes before deodorization, and also provided theoretical basis for oil refining industry to control the oil quality.