•The oil yield of Trichosanthes kirilowii Maxim seed oil increased with microwave heating time.•Antioxidant activity and the total phenolic increased with microwave heating time.•The tocopherol was highest with microwave heating for 2 min in the seed shell oil. Trichosanthes kirilowii Maxim seed is a primary source of edible vegetable oil and possesses a high nutritional value, making them extremely beneficial to humanity. To promote the extraction process of Trichosanthes kirilowii Maxim seed oil, the effect of microwave heating time (700 W for 0, 2, 4, and 6 min) on lipid composition, chemical properties, and antioxidant activity of oils was studied. The results showed that the oil yield of the seed increased with the microwave heating time. Besides, microwave heating time significantly affects (p < 0.05) DPPH and tocopherols, and the IC50 value of DPPH was highest with microwave heating for 6 min, whatever the shells are reserved. The tocopherol content was highest with microwave heating for 2 min in the seed shell oil, which was 1930.60 mg/kg. The longer microwave heating time could improve the oil yield and antioxidant activity of Trichosanthes kirilowii Maxim seed oil. The seed shell also affects chemical properties, fatty acid composition, antioxidant activity, and tocopherol contents of the Trichosanthes kirilowii Maxim seed oil. The Trichosanthes kirilowii Maxim seed shell oil has higher DPPH and tocopherols contents than seed kernel oil, while seed kernel oils showed higher oil yield and acid value. Our finding is valuable for manufacturers to choose suitable means to produce Trichosanthes kirilowii Maxim seed oil of required qualities and chemical compositions for targeted use.