Objective: To investigate the correlation between the expression of HER2 and Ki67 in invasive breast cancer tissue and the efficacy of anthracycline chemotherapy as well as the clinical prognosis. Methods: The database predicted the mRNA expression of HER2 gene in invasive breast cancer and its association with Ki67. The mRNA expression of HER2 in FFPE tissue samples of 53 cases of invasive breast cancer was detected by Nanostring nCounter technology, and the expression level was compared with that of anthracycline chemotherapy. 222 cases of invasive breast cancer from 2008 to 2012 were collected to analyze the protein expression level of HER2 and Ki67, and the correlation analysis was conducted based on the clinicopathological data and the chemotherapy efficacy of the patients. Results: GEPIA database analysis showed that the mRNA expression of HER2 in invasive breast cancer tissues was higher than that in normal control tissues, and the mRNA expression of HER2 was correlated with the mRNA expression of Ki67. Nanostring nCounter detected HER2 mRNA positive 16/53 (30.19%) and negative 37/53 (69.81%) in the 53 cases of invasive breast cancer. In the HER2 positive patients, chemotherapy was effective in 3 cases (18.80%) and ineffective in 13 cases (81.20%). In the HER2 negative patients, chemotherapy was effective in 19 cases (51.35%) and ineffective in 18 cases (48.65%). By further reviewing the clinicopathological data of 222 cases of invasive breast cancer, the results showed that the invasive breast cancer patients with HER2-/KI67 + predicted better chemotherapy efficacy and prognosis. Conclusion: In patients with invasive breast cancer with negative HER2, the high expression of Ki67 predicted better chemotherapy efficacy, and HER2+/Ki67-andHER2-/Ki67+ predicted a better prognosis of patients with invasive breast cancer.