The invention discloses a processing and utilization method of cadmium exceeded rice. According to the method, polypeptide with good metal affinity (bone morphogenetic protein, BMP) and genes of high-activity maltooligosyl tehalose synthase (MTSase) and maltooligosyl trehalose tetrahydrolase (MTHase) are selected by semi-rational design and a verification experiment, artificial synthesis is conducted, metal affinity polypeptide with a sequence of SEQ NO.1, the MTSase with a sequence of SEQ NO.2, and the MTHase with a sequence of SEQ NO.3 are constructed, which are respectively displaced in gene engineering bacteria on the surface of pichia pastoris, and fermentation culture, centrifugal dewatering and freeze drying are conducted, respectively, so that three kinds of pichia pastoris gene engineering bacteria are obtained, then, the obtained pichia pastoris gene engineering bacteria are added into a hydrolyzate of cadmium-containing protein obtained by separation of cadmium-polluted rice and liquefied starch milk, respectively, cadmium removal or a catalytic reaction is conducted, then corresponding treatment is conducted, so that the purposes of removing cadmium from the cadmium-polluted rice, and producing polypeptide and trehalose products for food industry are achieved.