The effect of through-the-thickness stitching and incorporation of multiwalled carbon nanotubes (MWCNTs) on the flexural properties of three-dimensional (3D) carbon/epoxy composites was studied. The flexural strength of the carbon twill fabric composites was improved by stitching due largely to delamination suppression, whereas stitching negatively influenced the flexural strength of the carbon satin fabric composites due to stitch-induced irregularities and fiber breakages. The failure mode of the unstitched base (without MWCNTs) and unstitched nano-added structures involved fiber breakage, matrix cracking, and delamination, while the stitched base and stitched nano-added samples exhibited lateral matrix cracking, multiple warp, and stitch yarn breakages with less delamination compared with unstitched structures. The results showed that both stitching and the incorporation of MWCNTs improved the out-of-plane failure properties due largely to restricted delamination. Therefore, stitching and MWCNTs can effectively be used to increase the damage tolerance of carbon fiber/epoxy composite laminates.