The study of mechanistic interpretability aims to reverse-engineer a model to explain its behaviors. While recent studies have focused on the static mechanism of a certain behavior, the training dynamics inside a model remain to be explored. In this work, we develop an interpretable method for fine-tuning and reveal the mechanism behind learning. We first propose the concept of node redundancy as an extension of intrinsic dimension and explain the idea behind circuit discovery from a fresh view. Based on the theory, we propose circuit-tuning, a two-stage algorithm that iteratively performs circuit discovery to mask out irrelevant edges and updates the remaining parameters responsible for a specific task. Experiments show that our method not only improves performance on a wide range of tasks but is also scalable while preserving general capabilities. We visualize and analyze the circuits before, during, and after fine-tuning, providing new insights into the self-organization mechanism of a neural network in the learning process.