Citrus is an important cash crop in the world, and huanglongbing (HLB) is a destructive disease in the citrus industry. To efficiently detect the degree of HLB stress on large-scale orchard citrus trees, an UAV (Uncrewed Aerial Vehicle) hyperspectral remote sensing tool is used for HLB rapid detection. A Cubert S185 (Airborne Hyperspectral camera) was mounted on the UAV of DJI Matrice 600 Pro to capture the hyperspectral remote sensing images; and a ASD Handheld2 (spectrometer) was used to verify the effectiveness of the remote sensing data. Correlation-proven UAV hyperspectral remote sensing data were used, and canopy spectral samples based on single pixels were extracted for processing and analysis. The feature bands extracted by the genetic algorithm (GA) of the improved selection operator were 468 nm, 504 nm, 512 nm, 516 nm, 528 nm, 536 nm, 632 nm, 680 nm, 688 nm, and 852 nm for the HLB detection. The proposed HLB detection methods (based on the multi-feature fusion of vegetation index) and canopy spectral feature parameters constructed (based on the feature band in stacked autoencoder (SAE) neural network) have a classification accuracy of 99.33% and a loss of 0.0783 for the training set, and a classification accuracy of 99.72% and a loss of 0.0585 for the validation set. This performance is higher than that based on the full-band AutoEncoder neural network. The field-testing results show that the model could effectively detect the HLB plants and output the distribution of the disease in the canopy, thus judging the plant disease level in a large area efficiently.