In the present work, Large Eddy Simulation (LES) is employed to investigate the heat transfer performance and flow characteristic in a rectangular channel with three-row miniature square column vortex generators (MSCVGs) as Reynolds number varies from 3745 to 11,235. The height of the MSCVGs is less than the thickness of the boundary layer, and MSCVGs arrays arranged in the form of aligned and staggered. In aligned and staggered arrangements, the spanwise distance between adjacent MSCVGs in the same row is 100 and 200 wall units, respectively. The numerical result indicates that the wake induced by the MSCVGs arrays has an obvious impact on the boundary layer. The wakes induced by the MSCVGs in aligned and staggered arrangements act as the "restricted belt" and "restricted plate" respectively, which can particularly alter and adjust the original flow structures, velocity streaks and vortices in the boundary layer. For the aligned array arrangement, the wakes induced by MSCVGs can improve the heat transfer performance of the channel as well as obtain the drag reduction. For the staggered array arrangement, the frictional coefficient of the channel decreases by up to 11.95%, and the Nusselt number decreases slightly with the effective reduction of the frictional resistance. The overall performance coefficient of the channel with three-row MSCVGs in staggered or aligned arrangements are both greater than 1 in all considered Reynolds number ranges, which means that MSCVGs arrays can enhance the overall thermal performance of the channel.