Aiming at the problems of incomplete cleaning, low classification accuracy, high damage rate, and slow efficiency of Ruditapes philippinarum after capture ashore, an integrated cleaning and classification machine for Ruditapes philippinarum is designed in this paper. Combined with the morphological characteristics of Ruditapes philippinarum, by analyzing the movement of Ruditapes philippinarum in the screen barrel and between the brush roller, the classification mode of brush roller combined with high spray and drum screening is determined, and the design of drum screen, high-pressure spray, and brush roller is completed. The simulation analysis of the operation parameters of the integrated cleaning and classification machine is carried out by using EDEM discrete element simulation. The simulation results show that when the speed of the brush roller is 3 r/min, the speed of the drum screen is 15 r/min and the inclination angle of the drum screen is 3 °, the classification accuracy is 91%, and the prototype manufacturing and power device matching are completed. Under the above parameters, the classification accuracy can reach 91%, the damage rate of the Ruditapes philippinarum is about 1%-2%, and the sediment attached to the shell is cleanly washed. The integrated operation of the cleaning and grading machine for Ruditapes philippinarum with high efficiency and low loss is realized.