In the study, 96 samples of Gardenia jasminoids Ellis in different preparation methods were collected, including model building with 83 samples and validation with 13 samples. The reference analysis was performed using a HPLC method to determine the content of geniposide. Method for the quantification of geniposide in Gardenia jasminoids Ellis in different preparation methods with NIRS are studied by integral sphere of diffuse reflection. The spectral regions from 8 660 to 7 500 cm-1, from 6 650 to 5 600 cm-1 and from 4 900 to 4 000 cm-1 were selected for the calculation of the quantitative model. The spectral data of geniposide were processed using the second derivative and standard normal variate transformation (SNV). The quantitative model of geniposide was built based on partial least squares (PLS) method with main components (8) with 83 samples of Gardenia jasminoids Ellis. Finally, validation of the quantitative model was accomplished with 13 samples of Gardenia jasminoids Ellis in different preparation methods. The correlation coefficients(R2), the root meat square error of calibration(RMSEC), the root meat square error of prediction(RMSEP), the root meat square error of cross validation(RMSECV) and RMSEP/RMSEC of the calibration model in geniposide were 0992 85, 0240, 0254, 0386 91 and 106. The ratio of standard deviation of the validation set to standard error of prediction (RPD) from model validation was 881, the range of absolute deviation was -039%~023%. The model established has good predictability. Besides, experimental conditions also have impact on the testing results, including scan frequency, amount of measured sample, the number of replications and resolution determined by correlation coefficient method. What’s more, using first derivative spectra, second derivative spectra and near-infrared spectra of geniposide to confirm the spectral regions can distinct the spectral regions according to temperature differences humidity and moisture content. For the first time, a quantitative model with NIRS is established for rapid determination of geniposide in Gardenia jasminoids Ellis with different preparation methods. The quantitative model of geniposide was stable and reliable, which can rapidly and accurately determine the content of geniposide in Gardenia jasminoids Ellis with different preparation methods with NIRS simultaneously.