Flaxseed oil is a high nutrition oil, rich in ω-3 fatty acid, tocopherols and phenolic compounds. However, it is prone to oxidation due to its high unsaturation which needs pretreatments to be easily introduce to the market. In this study, flaxseed oil was converted to powder form by mixing with microcrystalline cellulose (MC) and thyme powder to produce flaxseed oil powder. For this purpose, 3 different levels of thyme powder (5%, 10% and 15% of oil) were mixed with oil, followed by mixing with different proportions of MC (50:50, 50:75, 50:100 (oil:MC)) and stored for 90 days at 25 °C and 4 °C. Results indicated that the total phenolic compounds (23.2–91.2 mg GAE/100 g), chlorophyll (9–63.6 mg/kg), and carotenoid (4.4–9.9 mg/kg) contents increased with the incorporation of thyme powder into the flaxseed oil on the first day in 25 °C and 4 °C. Also during 90 days storage, phenolic compound (21.8%), chlorophyll (32.5%) and carotenoid (24%) decreased in both 25 °C and 4 °C temperatures. The results confirmed that adding thyme powder to samples decreased acidity and peroxide value in compare with control. Using thyme as a natural antioxidant and also transforming the oil to powder form by MC increased the oxidative stability in compare with control. The produced high stable flaxseed oil powder has the potential to be used directly on food products like salads or to be used in different food formulations to fortify them with natural antioxidants and ω-3 essential fatty acids.