Sea buckthorn has strong physiological activities, which might be attributed to its flavonoid compounds. The heat treatment could speed up the transformation of the flavonoids, so it would affect the properties of the flavonoids. To explore the effect of the heat‐treating methods on the sea buckthorn pulp flavonoids, the flavonoid compositions, color and taste properties, and antioxidant activity, prepared by three heating methods, were investigated. The results showed that the extractable sea buckthorn flavonoids rose after heat treatment; the high temperature with high‐pressure treatment had the largest yield (3.66 ± 0.21 mg/ml). A total of 16 flavonoid monomers were identified in the sea buckthorn, the content of isorhamnetin‐3‐ O ‐rutinoside was the highest in the pulp (589.34 ± 4.72 µg/ml), the concentrations of eight monomers increased after heat‐treating, and the treating methods could significantly affect the contents of flavonoid monomers ( p < 0.05). The difference in color was positively correlated to the heat‐treating time and temperature ( p < 0.01); the ΔE value in high pressure with high temperature treatment was the largest (10.59). The heat treatment enhanced bitterness and acidity, while it greatly reduced the saltiness, umami, and sweetness ( p < 0.01). The stronger antioxidant capacity of the total flavonoids was accompanied by the higher temperature and longer time of heat treatment. The antioxidant capacity was closely correlated to the contents of flavonoid monomers. Therefore, the heat treatment boosted the content of the flavonoids, enhanced the taste, and improved the antioxidant properties. Practical Application: This study can provide suitable a method for improving the extracting efficiency, improving properties and biological activities of sea buckthorn pulp flavonoids, also provide directions for predicting the antioxidant activity by the flavonoid monomer contents.