Protein and total fat are two ingredients to measure the quality of corn. The aim of this study is to evaluate the quality of corn by the dual-component join determination through Fourier transform near infrared (FT-NIR) spectroscopic analysis. The calibration models were established by the systematic study performed respectively in the four regions of the whole range, the second overtone, the first overtone, and the combination. Whittaker smoother was introduced as an attractive alternative data preprocessing method. With the optimized parameters, Whittaker smoother indicates its priority for improving modeling results in any of the four regions. The predictive abilities were compared between the joint analysis of protein and total fat and the separate analysis of each single component by partial least squares (PLS) modeling. The uncertainty in parameter was further estimated for the linear models. It is suggested that the joint analysis of dual-component always leads to better predictive results, and also provided good evaluation results for the independent validation samples. For the joint analysis, the optimal region for protein was the combination (5400-4000 cm(-1)), and the optimal region for total fat was the first overtone (7200-5400 cm(-1)). The optimal PLS models also provided appreciate predictive performance for both protein and total fat. And the parameter uncertainty determination provided an acceptable estimate of the measured uncertainty for the FT-NIR analysis of corn. In general, the joint analysis of dual-component is a better strategy for FT-NIR analysis of corn, and it is hoped to be tested for other objects.