Large Language Model (LLM)-based multi-agent systems rely on optimized collaboration topologies to balance performance and communication costs. However, current methods struggle with the inherent stability-extensibility trade-off and often misalign computational budgets with query difficulty. We propose \textsc{ATOM}, an adaptive framework that generates budget-controllable collaboration graphs via a novel task-driven reinforcement learning paradigm. Inspired by atomic structures, \textsc{ATOM} employs a nucleus-electron hierarchy: it maintains a stable, offline-learned collaboration backbone (the nucleus) while dynamically activating query-conditioned agents (electrons) during inference. Crucially, a complexity-aware budgeting strategy aligns resource consumption with task demands by estimating query difficulty to strictly regulate electron instantiation. Extensive experiments across six diverse benchmarks demonstrate that \textsc{ATOM} achieves state-of-the-art performance while improving token efficiency by up to $30\%$ compared to strong baselines.

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