The invention belongs to the technical field of flour food processing, and particularly relates to a multi-grain instant noodle and a manufacturing method thereof. The preparation method comprises the following steps: multi-grain flour and high gluten wheat flour are used as main raw materials and are manufactured into the multi-grain instant noodle with modified starch, vital gluten, salts, dietary alkali, composite phosphate, and monoglyceride through processes of dough making, still standing, calendering, cutting, steaming, forming, drying and the like, wherein the multi-grain flour is a flour material sieved by a sieve of 100-150 meshes and is manufactured by one or the combination of mung beans, black soya beans, kidney beans, peas, broad beans, ormosia, maize, potatoes, and sweet potatoes being subjected to ultrahigh pressing, enzymolysis, germinating and/or superfine grinding and then drying and smashing. The multi-grain instant noodle manufactured by the method has the outstanding advantages of well nutrition and flavor, high raw material utilization ratio, low nutrient loss, good reconstitution property, modest crunch and elasticity, low fat content and the like.