In this work, a novel double-layer microfluidic device for enhancing particle focusing was presented. The double-layer device consists of a channel with expansion-contraction array and periodical slanted grooves. The secondary flows induced by the grooves modulate the flow patterns in the expansion-contraction-array (ECA) channel, further affecting the particle migration. Compared with the single ECA channel, the double-layer channel can focus the particles over a wider range of flow rate. Due to the differentiation of lateral migration, the double-layer channel is able to distinguish the particles with different sizes. Furthermore, the equilibrium positions could be modulated by the orientation of grooves. This work demonstrates the possibility to enhance and adjust the inertial focusing in an ECA channel with the assistance of grooves, which may provide a simple and portable platform for downstream filtration, separation, and detection.