Long chain-of-thought (LongCoT) has emerged as a powerful reasoning paradigm for enabling large language models (LLMs) to solve complex tasks through a systematic and thorough thinking phase. Although supervised fine-tuning (SFT) on high-quality LongCoT traces has proven effective to activate LongCoT abilities, we find that models trained in this way tend to overfit problem-specific knowledge and heuristics, leading to degraded out-of-distribution performance. To address this issue, we propose a Decoupled LongCoT Fine-Tuning (DLoFT) algorithm, which enables the model to learn generalizable LongCoT reasoning abilities while preventing overfitting to the reasoning content with problem-specific information. The key idea is to decouple the gradient into two orthogonal components: 1) a paradigm-relevant gradient corresponding to the general LongCoT paradigm and 2) a content-relevant gradient reflecting the problem-specific information, where only the former gradient is used to update model parameters. Specifically, by leveraging the unique two-phase composition (thinking and solution) of the LongCoT response, our gradient decoupling mechanism isolates the content-relevant gradient via a projection operation and separates the paradigm-relevant gradient through orthogonalization. Our DLoFT ensures the model concentrate on internalizing the LongCoT paradigm rather than memorizing problem-specific knowledge and heuristics. Extensive experiments demonstrate that our DLoFT significantly improves the generalization behavior of LongCoT abilities compared to SFT while maintaining strong in-distribution performance.