The present work studied the combination effect of physical drying with chemical modification of carbon nanotubes (CNTs) on some through-thickness properties of carbon fiber/epoxy composites. Different drying methods of heat drying and freeze drying were utilized to affect CNT organization form in carbon fiber/CNTs preforms and composites: The adoption of heat-drying method made CNTs more inclined to form aggregates accompanied with randomly scattered CNTs, while continuous CNT networks could always be assembled when freeze drying method was employed. The formation mechanism of such CNT networks was discussed, and could be described as "freeze drying within confined space." Chemical characteristic of CNTs was controlled by choosing different solutions of non-functionalized CNTs (NOCNTs) or hydroxyl-modified CNTs (OHCNTs). As a consequence, CNT networks modified composites, especially that with OHCNTs formed networks, displayed significantly better electrical performance than composites with CNT aggregates and scattered CNTs; NOCNT networks and scattered OHCNTs made the corresponding composites possess higher interlaminar shear strength (ILSS) value, whereas OHCNT networks impaired ILSS while enhancing flexural strength and modulus of composites.