This paper provides a multi-stage medical scheme selection process to obtain the suitable scheme in the referral system. Firstly, considering the uncertainty of the experts and physicians, the preference relations (PRs) under the probabilistic linguistic term environment are introduced to the system. Then, this paper checks the consistency of the PRs and selects out the inconsistent PRs. For the inconsistent one, this paper provides alternative evaluations by repairing the most inconsistent element. Then, let experts choose from the alternative evaluation set. Next, by introducing the Bonferroni mean (BM) operator and Choquet integral, this paper integrates the historical data and the evaluations with stage weights to obtain the comprehensive assessment. The weights are calculated by the provided discrete and continuous stage weight functions or the programming model. Finally, the medical scheme selection process for the lung cancer and its simulation experiment are investigated to demonstrate the effectiveness and application of provided methods. The simulation experiments on sensitivity analysis and comparative analysis with existing methods are also conducted to validate the provided method.