Traditional animation production usually requires a lot of manual operation, and requires a high degree of professional skills. This not only limits the efficiency of animation production, but also enhances the difficulty of animation production. In order to solve this problem, this paper analyzes the free connection algorithm of three-dimensional modeling animation, deeply understands and analyzes the development and research status of the existing three-dimensional modeling animation, and defines the research objectives and tasks. Through analyzing the realization process of free connection algorithm and the design idea of three-dimensional modeling animation, this paper carries on the algorithm design and implementation, and describes the specific practice of the algorithm applied to three-dimensional modeling animation. Through the experiment of the three-dimensional modeling animation of the free link algorithm, it is found that the time efficiency of the free link algorithm is higher when processing the above basic actions; The average implementation time is 19 ms; The average implementation time of complex actions was 47.5 ms. The free join algorithm shows high performance in handling basic motion such as translation, rotation and scaling. It provides more flexible and natural movements when dealing with complex character movements or physical interactions. Through the analysis of three-dimensional modeling animation free connection algorithm, this paper promotes the practical application of three-dimensional modeling animation free connection, opens up a new research direction, and has both theoretical and practical significance.