Protein conformational ensemble generation aims to efficiently characterize the structural variations accessible to a protein beyond a single static structure. Recent flow-based methods efficiently generate conformational ensembles, but they model coordinated structural variation implicitly, which can limit ensemble fidelity and hinder direct control. To address this limitation, we propose CoMoFlow, a controllable framework for generating protein backbone conformational ensembles by explicitly modeling collective variation. CoMoFlow constructs protein-specific collective modes from the equilibrium structure, learns the distribution of their coefficients across the molecular dynamics (MD) ensemble, and uses sampled collective variations to guide SE(3) flow matching through feature conditioning and prior recentering. Experiments on ATLAS and de novo proteins show that CoMoFlow improves reconstruction of MD conformational distributions and coordinated structural variation relative to strong flow-based baselines, while enabling direct control over targeted conformational changes.

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