Watercore is an internal physiological disorder affecting the quality and price of apples. Rapid and non-destructive detection of watercore is of great significance to improve the commercial value of apples. In this study, the visible and near infrared (Vis/NIR) full-transmittance spectroscopy combined with analysis of variance (ANOVA) method was used for online detection of watercore apples. At the speed of 0.5 m/s, the effects of three different orientations (O1, O2, and O3) on the discrimination results of watercore apples were evaluated, respectively. It was found that O3 orientation was the most suitable for detecting watercore apples. One-way ANOVA was used to select the characteristic wavelengths. The least squares-support vector machine (LS-SVM) model with two characteristic wavelengths obtained good performance with the success rates of 96.87% and 100% for watercore and healthy apples, respectively. In addition, full-spectrum data was also utilized to determine the optimal two-band ratio for the discrimination of watercore apples by ANOVA method. Study showed that the threshold discrimination model established based on O3 orientation had the same detection accuracy as the optimal LS-SVM model for samples in the prediction set. Overall, full-transmittance spectroscopy combined with the ANOVA method was feasible to online detect watercore apples, and the threshold discrimination model based on two-band ratio showed great potential for detection of watercore apples.