This paper investigates the dynamic response of two freely rotatable rigid square cylinders to two-dimensional laminar flow in a microchannel. The square cylinders are laterally pinned side-by-side in the microchannel with a single freedom of rotation. Finite volume method coupled with a dynamic mesh technique is developed and validated to reveal the detailed motion characteristics of the cylinders and nearby flow structures. Under small Reynolds number (Re = 50), both cylinders oscillate periodically. The oscillate curves (rotating angle v.s. time) are symmetrical with each other but with a certain phase difference. At Re = 150, both cylinders oscillate randomly. Under high Reynolds number (Re = 300), the two cylinders both keep rotating in the opposite direction with the velocity magnitude fluctuating drastically around 1.75. Important motion details are presented to understand the Fluid-Structure interaction mechanism under different Reynolds number, including the time history of rotating angles and rotating velocities, lift and drag coefficients on the cylinders, distribution of pressure around the cylinder sides. Both pressure-induced torque and the shear induced one are obtained and their contributions to both cylinders’ rotation characteristics are quantitatively evaluated. Vortex structures and streamlines around the cylinders at specific moments are also revealed in this paper to help understanding the fluid-structure interaction phenomenon.