As a secondary analysis method, reproducibility and reliability of near-infrared spectroscopy (NIRS) quantitative analysis are quite dependent on modelling process. In this paper, it is focused on outlier analysis for protein quantitative model of wheat based on NIRS. The purpose is to discuss the outlier effect in modelling process of complex sample set. The indicator of outliers is the deviation between two interpretative percentage curves in partial least squares regression (PLSR) modelling, when two percentage curves have significant deviation or departure point, the sample set should include the outliers. The innovative research work is the analysis and treatment of outliers. On the basis of sub-model ergodic calculation method, outliers can be gradually identified and picked-up. The standard deviation of model’s prediction residual is used as the reference graduation to distinguish the degree of deviation. According to the degree of deviation from sample population, outliers can also be divided into significant outliers, relative outliers and potential outliers. In this paper, the significant outliers of the sample set are about 7.8%, and the relative outliers are about 15.6%. The outliers will pull normal samples apart from the ideal fitting line and make the dispersity increase. No matter modelling with removed outliers or weighted samples, the purpose is to make the fitting results of quantitative analysis modelling more inclined to majority samples, while reducing or eliminating the impact of outliers.