Medical vision-language models (VLMs) have shown increasing potential for radiological image interpretation. Medical VLMs encode radiological images into visual representations that capture both anatomical and phenotypic information for diagnosis. Existing approaches improve pathological phenotype representations through semantic-guided representation alignment. However, pathological phenotypes arise as lesion-specific visual changes superimposed on underlying normal anatomy. Such semantic alignment approaches fail to model the phenotype-specific increment relative to the corresponding normal anatomical representation. To address this gap, we propose \textbf{$Δ$Representation}, a visual phenotype representation learning framework based on counterfactual reasoning for medical VLMs. It comprises \textbf{BaseAnatomy}, a geometry-supervised representation learning module, and \textbf{$Δ$Phenotype}, a counterfactual incremental representation learning module. BaseAnatomy provides fine-grained geometric supervision through spatial relationships across and within anatomical structures. $Δ$Phenotype computes the representation increment between lesion representations and their corresponding normal anatomical representations, and supervises increments associated with the same phenotype to cluster in the representation space. Experiments on \textit{ReXGroundingCT} and \textit{LIDC-IDRI} demonstrate that $Δ$Representation effectively structures pathological phenotype representations and improves lesion grounding and phenotype characterization accuracy in medical VLMs. Code is available at https://anonymous.4open.science/r/deltarep-CF6D.

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