The invention discloses nutritional flavored composite sauce and a preparation method thereof, and belongs to the field of food processing. The method comprises the following steps: peeling and screening raw material seeds, carrying out ultrasonic soaking with a fructo-oligosaccharide solution with a certain concentration, carrying out microwave baking treatment, and carrying out sauce grinding toobtain a sauce material A; performing screening, superfine grinding and 80-100-mesh screening on the removed raw material skin to obtain raw material skin powder, then adding the raw material skin powder into vegetable oil preheated to 80 DEG C, and performing uniform stirring to obtain a sauce B; adding the sauce B into the sauce A, performing uniform stirring, performing homogenizing to obtaina sauce C, performing microwave sterilization, performing cooling, and performing filling so as to obtain the nutritional flavored composite sauce. The method is simple in process, low in energy consumption and low in cost. The obtained product is good in flavor, good in stability, free of layering, high in safety, high in nutritional value, rich in essential fatty acid and easy to digest and absorb.