To predict the environmental risk of the gene flow of transgenic B.napus after commercialization, a protocol for assessing its compatibility risks was proposed by the fuzzy clustering analysis and fuzzy model identification along with the biometric theory. The protocol included four steps: the fuzzy clustering analysis of interspecific crossing compatibility of transgenic B.napus, the F test of the outcome of the fuzzy clustering analysis, ranking of the risk of the interspecific crossing compatibility, and identifying the risk ranks. At the final stage of the protocol, various methods for identifying risk ranks were proposed to accommodate different data collection situations, therefore this approach was more flexible than the rigid ranking by the traditional clustering analysis. Subsequently, the protocol was demonstrated in a case study of the experimental data of common B.napus, and six ranks of risks were established, and the risk rank of the interspecific compatibility was identified successfully in a crossing experiment of B.napus. These results proved that the protocol proposed was operational.