Moisture content (MC) and freshness undergo evident changes during the storage of loquat fruits and thus are important indices of loquat fruit quality. Conventional methods for assessing MC and freshness are typically destructive and time-consuming, and cannot provide distribution maps of MC in the whole loquats. In this study, the use of hyperspectral imaging (HSI) was investigated for rapid and non-destructive prediction of MC in loquats, and for the visualisation of their MC distribution maps. Furthermore, freshness level discrimination models for loquats at different storage times were established using partial least squares discriminant analysis (PLS-DA), multinomial logistic regression (MLogR), and back-propagation neural network (BPNN) classification models. MC was well-predicted, with the best residual predictive deviation (RPD) of 2.40. Using the best prediction model, the distribution maps of MC in loquats were visualised. Additionally, the competitive adaptive reweighted sampling (CARS)-BPNN model obtained superior discrimination performance, with 95.56% and 93.33% accuracy for the calibration and prediction sets. Our results show that HSI is a promising fast and non-destructive method for determining MC and freshness of loquats.