A multi-channel magnetic control system is provided, which is used for mixing fluids containing magnetic particles or separating magnetic species. In the multi-channel magnetic control system, a plurality of magnetic field switches are allocated to surround a plurality of channels, and the magnetization directions of the magnetic field switches are controlled to generate an uneven local magnetic field gradient, so as to achieve the purpose of fluid mixing or separating the magnetic species. This system can be also used as controllable flow resistance devices for magnetic fluids. Based on the demand of magnetic field distribution, overall or local control of the magnetic field switches can be executed to perform parallel processing over the multi-channel system of multi-dimensional allocation, so as to effectively save the processing time. The mixing or separation rate can be obtained via detecting residual magnetic species by magnetoresistive sensors arranged in inlets and outlets of channels.