Background <p>This study aimed to visually analyze the heterogeneity of vascularity and cellularity across different sub-regions of breast cancer using habitat imaging (HI) to predict human epidermal growth factor receptor 2 (HER2) expression and evaluate the effectiveness of neoadjuvant therapy (NAT) in breast cancer patients.</p> Methods <p>A retrospective analysis was conducted on 76 patients diagnosed with breast cancer. Diffusion-weighted imaging (DWI) and dynamic contrast-enhanced MRI (DCE-MRI) sequences were utilized to acquire MR images. Apparent diffusion coefficient (ADC), K^trans, K_ep, and V_e values were measured for each sub-region, and the percentage of each sub-region relative to the total lesion was calculated. Statistical analyses, including t-tests, rank-sum tests, chi-square tests, and Spearman correlation, were performed.</p> Results <p>Three distinct sub-regions within breast cancer lesions were identified through HI, characterized physiologically as: low vascularity–high cellularity (LV-HC), low vascularity–low cellularity (LV-LC), and high vascularity–low cellularity (HV-LC). Significant differences were observed in the proportions of these tumor sub-regions between HER2-positive and HER2-negative breast cancers. Additionally, HER2-low and HER2-zero breast cancers demonstrated statistical differences in the second sub-region (LV-LC). Furthermore, the proportion of the first sub-region (LV-HC) was negatively correlated with the efficacy of NAT in breast cancer patients.</p> Conclusions <p>Habitat imaging can identify distinct sub-regions within breast cancer lesions, providing a noninvasive imaging biomarker for predicting HER2 expression levels and assessing the efficacy of NAT in breast cancer patients.</p>