The invention provides a method for extracting hesperidin and pectin in young citrus fruits through continuous phase transition. Dried and smashed young citrus fruit raw materials are subjected to continuous phase transition extraction with ethanol or methanol, wherein extraction conditions are as follows: the extracting agent velocity is 30-150 L/h, extractive temperature is 30-90 DEG C, the extraction pressure is 0.2-1.8 Mpa, extraction time is 2-24 h, separating temperature is 40-95 DEG C, the separating pressure is 0.1-1.5 Mpa; then, the young citrus fruit raw materials for hesperidin extraction is subjected to continuous phase transition extraction with tertiary water with pH 2-7, wherein extraction conditions are as follows: the extracting agent velocity is 30-120 L/h, extractive temperature is 50-95 DEG C, the extraction pressure is 0.1-1.6 Mpa, extraction time is 1-10 h, separating temperature is 55-90 DEG C, the separating pressure is 0.1-1.2 Mpa. The method is high in extraction rate, strong in continuous operability, simple and convenient to carry out, safe, friendly to the environment, low in cost and suitable for large-scale industrial production.