Sugariness is one of the most important indicators to measure the quality of Syzygium samarangense, which is also known as the wax apple. In general, farmers used to measure sugariness by testing the extracted juice of the wax apple products. Such a destructive way to measure sugariness is not only labor-consuming but also a wasting of products. Therefore, non-destructive and quick techniques for measuring sugariness would be significant for wax apple supply chains. Traditionally, the non-destructive method to predict the sugariness or the other indicators of the fruits was based on the reflectance spectra or Hyperspectral Images (HSIs) using linear regression such as Multi-Linear Regression (MLR), Principal Component Regression (PCR), and Partial Least Square Regression (PLSR), etc. However, these regression methods are usually too simple to precisely estimate the complicated mapping between the reflectance spectra or HSIs and the sugariness. This study presents the deep learning methods for sugariness prediction using the reflectance spectra or HSIs from the bottom of the wax apple. A non-destructive imaging system fabricated with two spectrum sensors and light sources is implemented to acquire the visible and infrared lights with a range of wavelengths. In particular, a specialized Convolutional Neural Network (CNN) with hyperspectral imaging is proposed by investigating the effect of different wavelength bands for sugariness prediction. In the experiments, the ground-truth value of sugariness is obtained from a commercial refractometer. The experimental results show that using the whole band range between 400 nm and 1700 nm achieves the best performance in terms of Brix error. CNN models attain the Brix error of ±0.552, smaller than ±0.597 using Feedforward Neural Network (FNN). Significantly, the CNN’s test results show that the minor error in Brix interval 0-10°Brix and 10-11°Brix are ±0.551 and ±0.408, these results indicate that the model would have the capability to predict if sugariness is below 10°Brix or not, which would be similar to the human tongue. These results are much better than ±1.441 and ±1.379 by using PCR and PLSR, respectively. Moreover, this study provides the test error in each Brix interval within one °Brix, and the results show that the test error is varied considerably within different Brix intervals, especially on PCR and PLSR. On the other hand, FNN and CNN obtain robust results in terms of test error.