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Large language models (LLMs) excel in problem-solving but require training data with diverse reasoning processes. Existing methods mainly optimize instruction-response pairs but lack a systematic design for the underlying reasoning structure. This paper proposes RSS: a Reasoning Structure driven data Synthesis method. We first proactively develop a hierarchical GFlowNet to construct reasoning structures efficiently through a coarse-to-fine directed acyclic graph (DAG) growth process. Then reasoning DAGs are leveraged to actively guide the instruction generation via an iterative suggester-editor workflow and enhance response quality using a structure-aware strategy. Experiments show that LLMs trained on our synthetic datasets achieve 48.50%, 84.00%, 79.90% for AlpacaEval2, GSM8K and HumanEval, outperforming existing data synthesis methods.