Purpose: To investigate the relationship between hypoxia-inducible factor 1-alpha (HIF-1α), Twist family BHLH transcription factor 1 (TWIST-1), and β1 integrin (ITGB-1) expression and tumor stiffness, and evaluate performance of HIF-1α, TWIST-1, and ITGB-1 alone and in combination with Ki-67 for predicting pathological responses to neoadjuvant chemotherapy (NACT) in breast cancer (BC). Patients and Methods: This was a prospective cohort study of 104 BC patients receiving NACT. Tumor stiffness and oxygen score (OS) were evaluated before NACT by shear-wave elastography and optical imaging; HIF-1α, TWIST-1, ITGB-1, and Ki-67 expression were quantitatively assessed by immunohistochemistry of paraffin-embedded tumor samples obtained by core needle biopsy. Indexes were compared among different residual cancer burden (RCB) groups, and associations of HIF-1α, TWIST-1, ITGB-1, and Ki-67 with tumor stiffness and OS were examined. The value of HIF-1α, TWIST-1, ITGB-1, and Ki-67, and a possible new combined index (predRCB) for predicting NACT responses was assessed by receiver operating characteristic (ROC) curves. Results: HIF-1α, TWIST-1, and ITGB-1 expression were positively correlated with tumor stiffness and negatively with OS. Area under the ROC curves (AUCs) measuring the performance of HIF-1α, TWIST-1, ITGB-1, and Ki-67 for predicting responses to NACT were 0.81, 0.85, 0.79, and 0.80 for favorable responses, and 0.83, 0.86, 0.84, and 0.85 for resistant responses, respectively. PredRCB showed better prediction than the other individual indexes for favorable responses (AUC = 0.88) and resistant responses (AUC = 0.92). Conclusion: HIF-1α, TWIST-1, ITGB-1, and Ki-67 performed well in predicting favorable responses and resistance to NACT, and predRCB improved the predictive power of the individual indexes. These results support individualized treatment of BC patients receiving NACT.