A filter assembly in the upper stream of the spinneret was used to disturb the mesophase pitch (MP) melt flow during the spinning of precursor fibers. We studied the microstructure evolution mechanism of the MP-based carbon fibers during this process. Results showed that the use of filter assembly had a significant effect on the size of the split in the cross-section of carbon fibers. The split has been completely depressed in the carbon fibers spun with 50 layers of plain-weave. Selected area electron diffraction results showed that carbon fibers spun with 50 layers of plain-weave screens exhibited an apparent decrease of the orientational order of the (002) diffraction plane in both center and transition regions. The results of Raman spectroscopy indicated that, the size of graphitic microcrystalline domain in carbon fibers decreased with increasing the number of plain-weave screens in the filter assembly. Our studies confirmed the roles of the filter assembly in precursor fiber spinning to disrupt the mesophase domain formation in the MP melt and thus induce a reduced domain size.