Granulation is a physiological disorder of juice sacs in citrus fruit, causing juice sacs to become hard and dry and resulting in decreased internal quality of citrus fruit. Honey pomelo is a thick-skinned citrus fruit, and it is difficult to identify the extent of granulation by observation of the outer peel and fruit shape. In this study, a rapid and non-destructive testing method using visible and near-infrared transmittance spectroscopy combined with machine vision technology was applied to identify and estimate granulation inside fruit. A total of 600 samples in different growth periods was harvested, and fruit were divided into five classes according to five granulation levels. Spectral data were obtained for two ranges of 400–1100 nm and 900–1700 nm by visible and near-infrared transmittance spectroscopy. In addition, chemometrics were used to measure the chemical changes of soluble solid content (SSC), titratable acidity (TA), and moisture content (MC) caused by different granulation levels. Machine vision technology can rapidly estimate the external characteristics of samples and measure the physical changes in mass and volume caused by different granulation levels. Compared with using a single or traditional methods, the predictive performances of multi-category classification models (PCA-SVM and PCA-GRNN) were significantly enhanced. In particular, the model accuracy rate (ARM) was 99% for PCA-GRNN, with classification accuracy (CA), classification sensitivity (CS), and classification specificity (CSP) of 0.9950, 0.9750, and 0.9934, respectively. The results showed that this method has great potential for the identification and estimation of granulation. Multi-source data fusion and application of a multi-category classification model with the smallest number of input layers and acceptable high predictive performances are proposed for on-line applications. This method can be effectively used on-line for the non-destructive detection of fruits with granulation.