Lipid oxidation is the major form of deterioration in salted-dried fish during storage. We here studied the use of Stevia rebaudiana stem (SRS) waste for impeding lipid oxidation of salted-dried Pacific saury fillets during chilled storage. Compared with Vitamin C (VC), the SRS extract (0.2%) significantly delayed lipid oxidation of the salted-dried fish, as determined through assays of the peroxide value, conjugated diene, thiobarbituric acid reactive substances, and acid value; VC is commonly used in salted-dried products. The color results further confirmed the feasibility of the SRS extract in maintaining the quality of the salted-dried Pacific saury fillets. The antioxidant mechanism studies unveiled that the SRS extract exhibited a higher Fe2+-chelating ability than VC, whereas the extract exhibited lower DPPH and ABTS radical-scavenging abilities than VC. This indicated that the high efficacy of the SRS extract in retarding lipid oxidation may be attributable to its higher Fe2+-chelating ability. The in situ Fe2+-chelating assay conducted using confocal laser scanning microscopy further confirmed this conclusion. Potential functional phenolic compounds in the SRS extract were then profiled using the LC-MS method. The SRS waste extract can thus be applied as a natural antioxidant for delaying lipid oxidation of salted-dried fish.