The most commonly applied techniques to assess human epidermal growth factor receptor 2 (HER2) expression in breast cancer are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). HER2 detection by reverse transcription quantitative polymerase chain reaction (RT-qPCR) can provide standardized, objective and automated assessment and reflect the HER2 expression continuity. Currently, there is lack of sufficient evidence to validate whether RT-qPCR technique is more appropriate for the detection of HER2 low expression, especially ultra-low expression. Here, we primarily utilized RT-qPCR to differentiate HER2 true negative, ultralow and 1 +, and compare the clinicopathological features and prognosis between RT-qPCR and IHC. 136 breast cancer cases with HER2 0 or 1 + were collected, also included 21 cases with HER2 2 + FISH negative as well as 25 cases with HER2 positive during the same period for comparative analysis. Compared the mRNA levels based on IHC/FISH scores. The receiver operating characteristic (ROC) curve was utilized to determine the threshold for reclassification, and the clinicopathological characteristics and prognosis differences among IHC true negative, ultra-low and 1 + after re-classification by RT-qPCR were analyzed. The mRNA level significantly differed between the IHC 0 and 1 + groups (p < 0.001). The IHC 0 group was further divided into true negative and ultralow, there was no statistically significant difference in mRNA levels between true negative and ultra-low groups, while the difference between ultra-low and 1 + mRNA levels was statistically significant (p < 0.001). After reclassification of IHC true negative, ultra-low and 1 + by RT-qPCR, there were statistically significant differences in histological grade, ER, PR and TILs expression. There was no significant difference between DFS and OS in the two classification methods. RT-qPCR classification aids in distinguishing clinicopathological characteristics and can serve as a supplementary technique for detecting HER2-low by IHC.