The invention discloses a thixotropic slurry grouting system for a large-section rectangular pipe-jacking pipeline. The thixotropic slurry grouting system comprises a storage tank, a pressure pump, grouting pipes, valves, pipe sections and grouting holes. The pipe sections are combined into the large-section rectangular pipe-jacking pipeline according to a certain sequence. The grouting holes are formed in the walls of the pipe sections and run through the same. The grouting holes in each pipe section are uniformly distributed along the circumference of the pipe section; the grouting holes in adjacent pipe sections are distributed in a staggered manner along the axis of the pipeline; in other words, the grouting holes are formed in different positions of the adjacent pipe sections along the axis, so that the grouting holes are distributed in the staggered manner in the pipe-jacking pipeline along the axis. The thixotropic slurry grouting system for the large-section rectangular pipe-jacking pipeline has the advantages that grouting pressure and grouting amount are reduced and an effective slurry sleeve can be formed around the pipeline.