The global use of plastic continues to grow because of plastic packaging, becoming the largest contributor to environmental pollution. To solve this issue, we developed a three-dimensional (3D) printing packaging system with biopolymer for agricultural products to reduce plastic usage and solve the environmental pollution problem. To model the packaging materials according to the shape of a matsutake mushroom, data were obtained using a 3D scanner and relevant software. Then, 3D modeling was conducted using Fusion 360™ software. A digital light processing 3D printer was used to make the output, and printing speed was adjusted using chitubox® and used. Using biodegradable polylactic acid (PLA) resin and 3D scanners and printers, customized agricultural packaging materials were successfully fabricated. The biodegradability of the packaging material was confirmed through experimentation. This study is expected to reduce plastic usage and increase the marketability of high-value agricultural products by enhancing their storage capabilities.