Palm oil milling at high temperature degrades heat-sensitive phytonutrients. Therefore, this study evaluated the effect of mild thermal processing (<60 °C) on phytonutrient content, antioxidant capacity, and minor lipid constituents of crude palm oils (CPO). This study showed that the mild-heat pressed CPO contained 52% higher carotene and 57% higher squalene than the highheat pressed CPO (p < 0.05). Furthermore, the mild-heat pressed CPO showed 2.8 times greater antioxidants than the high-heat pressed CPO, which coincided with a higher polyphenol content preserved by the mild thermal process. Upon further investigation into the lipid profile of CPO, overall compositional differences by main and subclasses between treatments were not significant. Nevertheless, several species of galactolipids, polyketides, and sphingolipid derivatives were significantly higher in the mild-heat pressed CPO. Overall, this study suggests that the mild thermal process could preserve essential phytonutrients and minor lipids in palm oil, enhancing its antioxidant properties.