Application of acoustophoresis to cell and particle separation in microchannel filled with fluid medium has been drawing increasing attention in many disciplines in the past decades due to its high precision and minimum damage to the matters of interest. Previous studies on particle separation often rely on the size-dependent feature of the acoustic radiation force (ARF), while the acoustic streaming effect (ASE) is a hurdle as the particle size goes down. Sub-micron particles circulate according to the streaming vortices and become inseparable from the particles settled on the pressure node. Instead of suppressing the ASE, this study intends to utilize the combined effect of ARF and ASE on sub-micron particle sorting by altering the microchannel’s cross-sectional shapes. The roles of ARF and ASE on particles with 0.2um and 2um in radius in various cross-sectional shapes are studied numerically. The studied geometries include 1. rectangular, 2. trapezoidal, and 3. triangular. The results show that changing the cross-sectional shapes affects the acoustic field’s magnitude and distribution, the streaming patterns, the magnitude of streaming velocity, and the movement of sub-micron particles. In non-rectangular microchannel, sub-micron particles circulate towards and settle at the center of the streaming vortices. This phenomenon shows the potential to manipulate the streaming-dominant particles, thereby enhancing the acoustophoretic particle sorting performance.