Sclerotinia sclerotiorum, one of the major diseases infecting oilseed rape leaves, has seriously affected crop yield and quality. In this study, an indoor unmanned aerial vehicle (UAV) low-altitude remote sensing simulation platform was built for disease detection. Thermal, multispectral and RGB images were acquired before and after being artificially inoculated with Sclerotinia sclerotiorum on oilseed rape leaves. New image registration and fusion methods based on scale-invariant feature transform (SIFT) were presented to construct a fused database using multi-model images. The changes of temperature distribution in different sections of infected areas were analyzed by processing thermal images, the maximum temperature difference (MTD) on a single leaf reached 1.7 degrees Celsius 24 h after infection. Four machine learning models were established using thermal images and fused images respectively, including support vector machine (SVM), random forest (RF), K-nearest neighbor (KNN) and naïve Bayes (NB). The results demonstrated that the classification accuracy was improved by 11.3% after image fusion, and the SVM model obtained a classification accuracy of 90.0% on the task of classifying disease severity. The overall results indicated the UAV low-altitude remote sensing simulation platform equipped with multi-sensors could be used to early detect Sclerotinia sclerotiorum on oilseed rape leaves.