Targeting at the problem of structure characterization of 3D flexible woven preform, the macroscopic geometry of preform and the mesostructure of fiber bundle were studied. Based on the basic assumptions that the fiber cross section is rectangular, the fiber is straight, the structure of preform is uniform, and the winding area between edge guide sleeve and fiber is ignored, the macroscopic geometric structure model of the preform was established, and the rationality of the model was verified by the weaving experiment. Through the densification and compaction process of the woven layer, the preforms with fiber volume fractions of 44.1%, 50.0%, and 52.5% were woven, and composite material samples were prepared using resin transfer molding (RTM) technology. After grinding and polishing, the mesomorphology of X/Y fiber bundles along Z direction and axial section was observed under microscope, as the sandwich area between Z direction fiber and X direction fiber or between Z direction fiber and Y direction fiber is defined as region A, and the orthogonal stacking region between X direction fiber and Y direction fiber is defined as region B. The results show that, under the influence of different compaction loads, the cross-sectional morphology of the X/Y direction fiber bundle in the A region for the preform with high fiber volume fraction tends to be more rectangular. The cross-sectional morphology of the X/Y direction fiber bundles in the B region shows a slight reverse semicircle shape when the fiber volume fraction of the preform reaches 50%, and it is approximately rectangular when the fiber volume fraction reaches 52.5%. The axial cross-section observation results of the X/Y fiber bundles show that the axial cross-sectional morphology of the fiber bundles in the A and B regions respectively form anti-drum and drum structures, which alternately and repeatedly appear along the fiber bundle axis. With the increase of compaction load, the fiber volume fraction of the part increases, and the above characteristics are more obvious. By analyzing the mesostructure characteristics of carbon fiber preform, the influence of compaction degree on the mesostructure of the preform was obtained, which provides a reference for predicting the performance of the composite materials.