An ω-3 and ω-6 fatty acid balanced pumpkin-flaxseed oil was prepared by mixing the seeds of seed purpose pumpkin in Xinjiang as raw material and flaxseed, a specialty oilseed crop in Xinjiang, as auxiliary material and then pressing them or the reverse sequence as a control and was refined. Changes in the physicochemical properties, nutritional composition, fatty acid composition, and oxidative stability of the two blended oils were studied before and after refining. The results showed that the physicochemical properties of the refined oils were significantly improved when compared with those of the crude oils (P < 0.05), and all quality indexes met the requirements of the national standards for edible oil. There were no differences in physicochemical indexes between the crude oils and between the refined oils (P > 0.05). The composition and content of fatty acids did not significantly change before and after refining (P > 0.05), while the contents of total tocopherol and total phenol and oxidative stability significantly decreased (P < 0.05). Compared with the control, the crude and refined oils prepared by mixing and then pressing had higher contents of total tocopherols and total phenols and better oxidative stability (P < 0.05), thus being more advantageous. The results of this study provide a theoretical basis for the market development of pumpkin seed oil.