In this study, we used fluorescence and absorption spectra to compare the conformation difference of BR protein of blue and purple membrane and to discuss the effect of temperature on conformational changes at room temperature.The endogenous fluorescence spectra studies indicate that the maximum emission wavelengths of tryptophan fluorescence in blue and purple membrane proteins at room temperature are 340 nm, and the fluorescence quantum yield of blue membrane is about 1.4 fold higher than that of purple membrane.The maximum emission wavelengths of bacteriorhodopsin fluorescence in blue and purple membrane at 280 nm are 331 nm and 326 nm respectively.The endogenous fluorescence is came from the dedication of tryptophan and tyrosine together and the fluorescence is mainly came from the action of tyrosine in purple membrane.The binding study of extrinsic fluorescent probe bis-ANS indicated that the probe Can bind only to BR in blue membrane, but not to BR in purple membrane.