A multi-field coupled model was developed to simulate the flow–compaction behavior of thick composite laminates manufactured by the autoclave process based on Darcy’s law and the effective compaction stress theory. The model was verified by comparing the predictions with the experiment results of a thick unidirectional laminate. The results show that the resin flow and compaction of fiber bed start from the top surface and gradually spread into the interior region, and the non-uniform resin flow along the thickness direction causes a gradient distribution of fiber volume fraction in the thick composite part. A cross-plied composite laminate model with a thin interlaminar layer was constructed, and the effect of the interlaminar transverse permeability on the flow–compaction behavior of the thick cross-plied laminate was numerically analyzed. The results indicate that the thick cross-plied composite laminate with high interlaminar transverse permeability has the similar flow–compaction process with that of the thick unidirectional laminate. An interlaminar layer with low transverse permeability impedes the resin flowing out from the interior of the thick cross-plied composite laminate and causes a lower fiber volume fraction compared with that in a unidirectional laminate.