The invention discloses a magnetic resonance multichannel digital transmission system, including a multipath data multiplexing unit, a data encapsulation unit, a high speed serial transmission unit, a fiber transmission unit, a fiber reception unit, a high speed serial reception unit, a data unpacking unit and a multipath data demultiplexing unit. Multichannel magnetic resonance digital signals after sampling and front-end processing are subjected to multiplexing according to magnetic resonance data word lengths, obtained data of all channels are polled as a frame, and frame synchronization codes required in demultiplexing are inserted at a frame header, and thus the real-time property and the integrity of magnetic resonance data are ensured. Synchronous clock information is inserted in line coding, and thus transmission of magnetic resonance data and clock can be completed using a single channel, and system equipment is simplified. FPGA chip programming realization is used to improve the system integration degree. The invention also provides a magnetic resonance multichannel data transmission method.