Near infrared spectroscopy (NIRS) is based on molecular overtone and combination vibrations. It is difficult to assign specific features under complicated system. So it is necessary to find the relevance between NIRS and target compound. For this purpose, the chondroitin sulfate (CS) ethanol precipitation process was selected as the research model, and 90 samples of 5 different batches were collected and the content of CS was determined by modified carbazole method. The relevance between NIRS and CS was studied throughout optical pathlength, pretreatment methods and variables selection methods. In conclusion, the first derivative with Savitzky–Golay (SG) smoothing was selected as the best pretreatment, and the best spectral region was selected using interval partial least squares (iPLS) method under 1mm optical cell. A multivariate calibration model was established using PLS algorithm for determining the content of CS, and the root mean square error of prediction (RMSEP) is 3.934 g·L^-1. This method will have great potential in process analytical technology in the future.