Objective To compare thickness and gap width between direct 3D-printed clear aligners (DPA) and conventional thermoformed aligners (TFA), providing experimental evidence for clinical application of clear aligners. Methods Sixteen adult subjects with mild dental crowding and without significant caries or restorations were recruited. For each subject, clear aligners were fabricated using direct 3D printing and conventional thermoforming methods, respectively. The aligner thickness was measured at labial/buccal and lingual surfaces of incisors, canines, and first molars using a high-precision electronic thickness gauge. Micro-CT scanning was employed to analyze the gap between the aligners and dental models. Statistical analyses were subsequently performed. Results The overall mean thickness of DPA aligners was (0.60±0.04) mm, significantly higher than TFA aligners (0.48±0.06) mm (P<0.0001), with superior thickness uniformity. The average gap between DPA aligners and dental models was (0.29±0.08) mm, significantly smaller than TFA aligners (0.31±0.16) mm (P=0.03), particularly at incisal edges of incisors, buccal surfaces of canines, and occlusal surfaces of first molars (P<0.05). Conclusion Compared to conventional thermoformed aligners, direct 3D-printed clear aligners using DCA material demonstrate significant advantages in thickness uniformity, fitting accuracy, and adaptability at clinically relevant regions, indicating greater potential for orthodontic clinical application.