Molecular subtypes and Nottingham Prognostic Index (NPI) are both prognostic models for breast cancer patients. We evaluated the association between molecular subtypes and NPI in 1042 breast cancer patients. The molecular subtypes indicating poorer prognosis were positively correlated to higher NPI (r = 0.138, P = 0.001). ER positive expression and PR high expression were positively correlated with NPI (r = 0.142, P = 0.001; r = 0.139, P = 0.001; respectively) and negatively correlated with histological grade (r = -0.233, P < 0.001; r = -0.176, P < 0.001; respectively). Ki67 status was negatively correlated with NPI and positively correlated with histological grade (r = -0.120, P = 0.004; r = 0.197, P < 0.001; respectively). The percentages of cases with NPI score 2.00-3.40 were higher in the luminar A, ER+, PR high expression and Ki67 low expression group, and the percentages of cases with NPI > 5.40 were higher in the HER2 overexpression subtype, basal-like subtype, ER-, PR low/negative expression, and Ki67 high expression groups. The excellent consistence was observed between histological grade and molecular subtypes, ER, PR, Ki67. The difference of histological grade between the HER2 positive and negative group was statistically significant. In conclusion, there was closely association between molecular subtypes and NPI in breast cancer. For further comparing the prognostic significance of molecular subtypes and NPI, survival analyses should be performed on the same population in a large-scale prospective study.