Accumulating evidence has shown that soy intake is associated with the promotion of health and prevention of cancers. However, the relationship between the intake of soy compounds and the risk of breast cancer is still debatable. In this study, we use mathematical models for assessing the impact of soy phytoestrogens and protein/peptide intervention on breast cancer development using the datasets acquired from a large number of published studies. We used data mining models, including the decision tree classification and association rule methods, to analyze 478 data collected from 201 research papers. The results indicated that the intervention of soy proteins and peptides, especially lunasin (LUN) and bowman-birk protease inhibitor (BBI), has a positive impact on different types of breast cancer, while the effects of soy phytoestrogens are inconsistent in breast cancer development. Among soy phytoestrogens, daidzein (DAI) exhibited the highest negative impact on breast cancer, followed by coumestrol (COU), soysapogenol (SAP), genistein (GEN), and equol (EQ). With regard to the type of cancer, phytoestrogens should be carefully considered in estrogen receptor (ER)+ or progesterone receptor (PR)+ breast cancer. In the case of ER−, PR− or triple negative type, both soy categories can be used as auxiliary interventions. In summary, this is the first study to use data mining to explore the relationship between the intake of soy phytoestrogens or proteins/peptides and breast cancer development. Our findings indicate that soy intervention might reduce breast cancer development. However, the specific soy compound and cancer type should be considered before allocating a precise nutrient intervention.