Background: Retention is a critical aspect of orthodontic treatment with aligners as it counteracts vertical displacing forces and ensures greater predictability of tooth movement. The aim of this study is to evaluate and compare the retention effectiveness of 3D-printed aligners and thermoformed aligners, analyzing how margin design and thickness gradients affect retention under different occlusal conditions. Methods: Tensile tests were conducted using a Sauter TVO-A01 machine, recording the force required to displace each aligner from the models. Quantitative data on the retention force of each aligner were collected based on malocclusion type and design specifics. Results: Scalloped thermoformed aligners demonstrated significantly lower retention values (p = 0.029) compared to 3D-printed aligners with high margins with horizontal and vertical gradients. Scalloped margin aligners exhibited significantly lower retention values (p = 0.008) compared to straight margin aligners. Additionally, 3D-printed aligners with uniform thickness gradients had significantly lower retention values (p = 0.040) compared to thermoformed aligners. Conclusions: The 3D printing production process enables customizable designs tailored to the unique characteristics of each patient. High-margin 3d-printed aligners with horizontal and vertical gradients provide superior retention, particularly in complex clinical situations such as dental crowding.