Model performance of the partial least squares method (PLS) alone and bagging-PLS was investigated in online near-infrared (NIR) sensor monitoring of pilot-scale extraction process in Fructus aurantii. High-performance liquid chromatography (HPLC) was used as a reference method to identify the active pharmaceutical ingredients: naringin, hesperidin and neohesperidin. Several preprocessing methods and synergy interval partial least squares (SiPLS) and moving window partial least squares (MWPLS) variable selection methods were compared. Single quantification models (PLS) and ensemble methods combined with partial least squares (bagging-PLS) were developed for quantitative analysis of naringin, hesperidin and neohesperidin. SiPLS was compared to SiPLS combined with bagging-PLS. Final results showed the root mean square error of prediction (RMSEP) of bagging-PLS to be lower than that of PLS regression alone. For this reason, an ensemble method of online NIR sensor is here proposed as a means of monitoring the pilot-scale extraction process in Fructus aurantii, which may also constitute a suitable strategy for online NIR monitoring of CHM.