Postoperative volume changes in reconstructed flaps are known to influence the functional restoration of resected areas of the upper aerodigestive tract. The purposes of this study were to estimate the volume decreases in flaps and investigate clinical factors affecting the volume decrease. The medical records of 19 patients who underwent ablation and flap reconstruction surgeries for head and neck cancers were reviewed. The volume of the reconstructed flap was measured at 3, 12, and 24 months postoperatively using CT or MR imaging and the 3D-DOCTOR software. The relationships between volume changes and perioperative clinical parameters were examined. The primary tumor locations were the nasal cavity and paranasal sinus, oropharynx, oral cavity, and hypopharynx in 8, 6, 4, and 1 case, respectively. Twelve patients underwent anterolateral thigh flap (ALTF) reconstruction, and seven patients underwent pectoralis major myocutaneous flap (PMMCF) reconstruction. Twelve (63.2%) patients received postoperative radiation. The estimated volume decreases at 12 and 24 months postoperatively for ALTF were 20.9 and 24.8%, respectively, while those for PMMCF were 7.3 and 10.8%, respectively. Among clinical factors, only the type of flap affected the volume change. When determining the volume of reconstructed flaps, the type of flap must be considered. It was recommended to make free and regional flaps at least 20 and 10% larger, respectively than the actual defect.