Objective To seek the statistical solution in the comparison of different effects from multi-center randomized controlled trials （RCTs）. Methods The data collected from a multi-center RCT were used as the examples and processed by CMH test and meta-analysis. Results The result of CMH test indicated that the significant difference of the effect values existed among centers （P 〈0. 05 ）. While meta-analysis showed no significant difference （P 〉0.05 ） by heterogeneity test. However, when using fixed effect model, inter-group significant difference of merged effect values was observed （P 〈0.05 ）. Conclusions In the clinical research based on the method of multi-center RCT, met.a-analysis can be applied if the difference of inclination of the inter-group therapeutic effect is found among different centers. The proper mathematical model should be selected based on the result of heterogeneity test to merge and compare the effect values. The conclusions should be drawn from the results of both meta-analysis and CMH test.