To provide a method and system for enabling easy separation of citrus fruit seeds to be utilized for production of the citrus fruit seeds themselves or a combination of the seeds and respective structures (composed of fruit skin, inner bags, fruity flesh and the like) other than the fruit seeds.

The system for separating citrus fruit seeds 1 is provided with a copper pressure cooker 4 as a pressure boiler boiling citrus fruits 3 having seeds 2 under pressure, a fruit storage body 6 having a plurality of holes 5 each having such a size as not to pass the seeds 2 of the fruits 3 and storing the fruits 3 boiled under pressure with the pressure cooker 4, a tank 8 in the inside of which the fruit storing body 6 storing the fruits 3 and liquid 7 are arranged, a rotary power-imparted means 9 alternately applying normal rotational force and reverse rotational force on the fruits 3 stored in the fruit storing body 6 via the liquid 7 in the tank 8; and a fruit beating means 10 beating the fruits 3 boiled under pressure with the pressure cooker 4.