There has been no study on using near-infrared spectroscopy (NIRS) to predict the hotness of fresh pepper. This study is aimed at developing a non-destructive and accurate method for determining the hotness of fresh peppers using portable NIRS and the variable selection strategy. Spectra from different locations on samples were obtained non-destructively with a single scan. Quantitative models were established using partial least squares (PLS) with a variable selection method or fusion method. The results showed that near-stalk was the best spectral acquisition location for quantitative analysis. The variable selection strategy allows the selection of targeted characteristic variables and improves the results. A fusion method, namely variable adaptive boosting partial least squares (VABPLS), was selected for optimal prediction of the performance. In the optimized model, the root mean square errors of prediction for the validation set (RMSEPvs) of capsaicin, dihydrocapsaicin and pungency degree were 0.295, 0.143 and 47.770, respectively, while the root mean square errors of prediction for the prediction set (RMSEPps) collected one month later were 0.273, 0.346 and 75.524, respectively.