In the present paper, both the physical characteristics and spectral signatures of southern Xinjiang jujube were studied. With the methods of repetitive adjustment and stepwise refinement, the analysis diagram of jujube quality subdivision and characteristic factors were obtained. In actual practice, the spectra repeatability and quality can be improved by setting an optimum acquisition parameter according to different experimental requirements. Through experiments the characteristic factors of crack browning, luster and compositions were obtained, which demonstrates a distinguishing downing characteristic spectral line at the wave number of 10 170 cm-1. Through characteristic analysis of jujube NIR spectra, the correspondence between the jujube spectra and their qualities was established, which lays the foundation for jujube qualities’ characteristic coding in the future. The application of near-infrared topology method in the quality analysis of southern Xinjiang jujube is cost saving, which has a broad application prospect in establishing the NIR analytical standard and model database sharing of the jujube’s quality in the future.