Abstract: An enzyme linked immunosorbent assay(ELISA) quantitative method has been established to analyze Cry proteins extracted from transgenic Bt cotton. Various molecular biological methodologies such as gel electrophoresis, ordinary polymerase chain reaction(PCR) and real-time fluorescence quantitative PCR were applied to detect Bt gene in transgenic cotton qualitatively and quantitatively. Both standard curves of Bacillus thuringiensis insecticidal crystal protein Cry1Ab and Cry1Ac proteins in the ELISA analysis were of good linearity with correlation coefficients(r²) of > 0.999, and the relative standard deviations(RSD) for the analyses were less than 2%. The newly established method is easy to operate, rapid, reproducible and precise, and it can be used in the fields of agro-food industry and environmental science to analyze Bt toxin proteins in genetically modified crops.