Particle manipulation using ultrasonic standing waves has gained increased attention in recent years as it is efficient and noninvasive. In order to predict the effects of acoustic streaming on the concentration of particles in the actual microchannel geometry, this paper presents a 3D numerical study on the transient motion of microparticles suspended in a liquid-filled microchannel, considering the mixed standing and traveling waves. The motion was generated by the acoustic radiation force and acoustic streaming-induced drag force arising from an imposed bulk acoustic wave and the hydrodynamic drag. The acoustic streaming patterns in the 3D microchannel were investigated using the limiting velocity method. In addition, the effects of the 3D streaming pattern in an acoustofluidic device on the acoustophoretic motion of microparticles were evaluated. The concentration of polystyrene particles was simulated for many particles with diameters of 0.5, 2, and 5 μm released from random initial locations. The obtained results indicate a balance between the flow rate and the particle diameter to achieve the highest concentration percentage. Increasing the height increased the concentration of large 5-μm-diameter particles to more than 80%. By doubling the length of the piezoelectrically actuated region, the concentration of 2-μm particles improved by approximately 20%. Finally, increasing the viscosity of the fluid by using a 50% glycerol-in-water mixture resulted in a greater effect of acoustic streaming. This study can provide helpful guidance for optimizing the design of acoustofluidic devices to enhance experiments.