The determination of a treatment plan for a target patient with tumor is a difficult problem due to the existence of heterogeneity in patients’ responses, incomplete information about tumor states, and asymmetric knowledge between doctors and patients, and so on. In this paper, a method for quantitative risk analysis of treatment plans for patients with tumor is proposed. To reduce the impacts of the heterogeneity in patients’ responses on analysis results, the method conducts risk analysis by mining historical similar patients from Electronic Health Records (EHRs) in multiple hospitals using federated learning (FL). For this, the Recursive Feature Elimination based on the Support Vector Machine (SVM) and Deep Learning Important FeaTures (DeepLIFT) are extended into the FL framework to select key features and determine key feature weights for identifying historical similar patients. Then, in the database of each collaborative hospital, the similarities between the target patient and all historical patients are calculated, and the historical similar patients are determined. According to the statistics of tumor states and treatment outcomes of historical similar patients in all collaborative hospitals, the related data (including the probabilities of different tumor states and possible outcomes of different treatment plans) for risk analysis of the alternative treatment plans can be obtained, which can eliminate the asymmetric knowledge between doctors and patients. The related data are valuable for the doctor and patient to make their decisions. Experimental studies have been conducted to verify the feasibility and effectiveness of the proposed method.