A method for preparing cassava flour with a low content of cyanogenic glycosides is provided. The method includes: washing, peeling, and cutting newly harvested fresh cassava to obtain cassava pellets, cassava shreds, or a cassava pulp as a raw material. The method further includes the following steps: immersing the raw material in a solution containing cellulase and pectinase for 10-30 minutes, and then placing the raw material in warm water with a temperature of 35-50° C. and a pH value of 5.5-6.5 and ultrasonicating for 10-30 minutes at an ultrasonic frequency of 50-80 kHz, to obtain an ultrasonicated raw material; drying and pulverizing the ultrasonicated raw material to obtain cassava flour with a low content of cyanogenic glycosides, a cyanogenic glycoside content of the cassava flour is less than 15 mg/kg.