Hainan/Eksotika papaya is a popular cultivated plant in Hainan Island, China. Papaya seed oil (PSO) contains functional compounds with good antioxidant activity, especially monounsaturated fatty acids. In this work, the ultrasound‐assisted extraction (UAE) of PSO was optimized using response surface methodology. It was found that the optimal extraction performance was realized when the elevated time was set to 20 min, the ultrasound power was set to 250 W, and the n‐hexane‐to‐sample ratio was set to 16:1 (v/w). The highest yield of PSO (32.27%) was obtained under the optimal conditions, and PSO showed good oxidative stability. Differential scanning calorimetry analysis showed that the melting point of Hainan/Eksotika PSO was low, while its crystallization temperature was high. FTIR and NMR were used to analyze the chemical structure of PSO, which also proved that PSO possessed good stability without oxidative degradation. In addition, scanning electron micrograph was employed to investigate the change in seed microscopic structure. The results showed UAE caused serious structural damage of sample cell membranes and walls, which help oil access to the solvent with a high extraction ratio. The results indicated that UAE is an efficient environmental‐friendly, and promising technique could be applied to produce PSO or other edible oil with a better health‐beneficial value in food industry.