Disclosed is a method for multi-center effect compensation based on a PET/CT intelligent diagnosis system. The method includes the following steps: estimating multi-center effect parameters of a test center B relative to a training center A by implementing a nonparametric mathematical method for data of the training center A and the test center B based on a location-scale model about additive and multiplicative multi-center effect parameters, and using the parameters to compensate the data of the test center B to eliminate a multi-center effect between the test center B and the training center A. According to the present disclosure, the multi-center effect between the training center A and the test center B can be compensated, so that the compensated data of the test center B can be used in the model trained by the training center A, and the generalization ability of the model is indirectly improved.