Under the trend of globalization and medical globalization, the popularity and circulation of medical information enhance the competition in medical industry that the cross-national-border medical behavior pattern is emerged. In comparison with high medical expenses and long waiting time in European and American countries, healthy medical service and quality and lower medical expenses in Asian countries facilitate the citizens in European and American countries seeking medical care in Asian countries. Medical tourism is therefore generated. The performance evaluation of medical ecology system in tourism development is therefore studied. With the computation of Modified Delphi Method, the geometric mean is regarded as the expert consensus about the evaluation of inputs and outputs to select the factors being able to evaluate the performance of medical ecology system in tourism development. Moreover, DEA is applied to measure the performance of medical ecology system in tourism development. With strict selection, total 16 Shanghai city-governed districts are selected as the samples. The research results show 1 DMU presenting strong efficiency on medical ecology system in tourism development, 5 DMUs revealing the efficiency between 0.9 and 1 on medical ecology system in tourism development, and 10 DMUs appearing the efficiency lower than 0.9 on medical ecology system in tourism development. According to the results, suggestions are proposed in this study, expecting to make real contributions to domestic medical ecology system in tourism development.