Shear thickening of multimodal suspensions has proven difficult to understand because the rheology depends largely on the microscopic details of stress-induced frictional contacts at different particle size distributions (PSDs). Our discrete particle simulations below a critical volume fraction ϕc over a broad range of shear rates and PSDs elucidate the basic mechanism of order–disorder transition. Around the theoretical optimal PSD (relative content of small particles ζ1= 0.26), particles order into a layered structure in the Newtonian regime. At the onset of shear thickening, this layered structure transforms to a disordered one, accompanied by an abrupt viscosity jump. Minor increase in large-large particle contacts after the order–disorder transition causes apparent increase in radial force along the compressional axis. Bidisperse suspensions with less regular but stable layered structure at ζ1= 0.50 show good fluidity in the shear thickening regime. This work shows that in inertial flows where particle collisions dominate, order–disorder transition could play an essential role in shear thickening for bidisperse suspensions.