The animation market is experiencing significant growth and diversification, with an expanding audience base and increasingly sophisticated aesthetic demands. This paper presents the development of a digital media art animation design system, leveraging four pivotal 3D technologies: mesh space deformation, 3D coordinate transformation, keyframe interpolation, and model collision detection. The system is enhanced with modules for scene editing, particle systems, and animation editing, which decompose the intricate special effects design of digital media art animations into manageable, editable components that offer real-time feedback. Furthermore, the system’s rendering capabilities and the animation design’s visual appeal were subjected to empirical evaluation. The findings indicate that within a 3D technology framework, the animation designs achieved average scores of 7.4371, 6.4720, and 7.0155 for recognizability, fidelity to the intended design, and overall impression, respectively, fulfilling the anticipated outcomes. Additionally, the animations produced are highly scalable and can be rendered swiftly and efficiently across diverse platforms. This study provides valuable insights for enhancing the effective deployment of 3D technologies in digital media art and animation design.