Universal sound separation faces a fundamental misalignment: models optimized for low-level signal metrics often produce semantically contaminated outputs, failing to suppress perceptually salient interference from acoustically similar sources. To bridge this gap, we introduce MARS-Sep, a reinforcement learning framework that reformulates separation as decision making. Instead of simply regressing ground-truth masks, MARS-Sep learns a factorized Beta mask policy that is optimized by a clipped trust-region surrogate with entropy regularization and group-relative advantage normalization. Concretely, we sample masks from a frozen old policy, reconstruct waveforms, and update the current policy using clipped importance ratios—yielding substantially more stable and sample-efficient learning. Multimodal rewards, derived from an audio-text-vision encoder, directly incentivize semantic consistency with query prompts. We further propose a progressive alignment scheme to fine-tune this encoder, boosting its cross-modal discriminability and improving reward faithfulness. Extensive experiments on multiple benchmarks demonstrate consistent gains in Text-, Audio-, and Image-Queried separation, with notable improvements in signal metrics and semantic quality.