Medication recommendation is a multi-label prediction task. However, existing prediction-set evaluation and calibration methods rely mainly on exact-overlap metrics and therefore treat all missed medications as equally severe, overlooking how closely the prediction set matches them within the medication hierarchy. To address this, we introduce Conformal Severity Control (CSC), a post-hoc framework for calibrating medication prediction sets under hierarchy-aware mismatch severity. CSC uses the Anatomical Therapeutic Chemical (ATC) hierarchy to quantify mismatch severity and controls patient-level severity without retraining the predictor, supporting both average severity and upper-quantile severity for the highest-severity mismatches. Experiments on MIMIC-IV show that CSC tracks user-specified severity tolerances and shifts prediction sets away from distant mismatches toward exact or close matches.

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