Some disease datasets have different degrees of missing, which will lead to the problem of low classification accuracy. To improve the effectiveness of breast cancer disease detection and diagnosis, a classification prediction method combining KNNI and XGBoost was proposed and applied to the classification and analysis of breast cancer data. First, the KNNI method is used to impute the missing data in the breast cancer patient dataset; Then, the original dataset is equalized by the SMOTE oversampling method; Finally, XGBoost is used to extract features that are strongly related to breast cancer malignancies as the input of the model, optimize the XGBoost model by grid search algorithm, find the optimal model parameters, and classify and diagnose the breast cancer dataset. The experimental results show that KNNI can effectively recover the lost data, improve the data quality, and improve the subsequent classification accuracy. Applying imputation methods to flexibly apply missing data to machine learning methods holds great promise.