Airborne fungal spores have always played an important role in the spread of fungal crop diseases, causing great concern. The traditional microscopic spore classification method mainly relies on naked eye observations and classification by professional and technical personnel in a laboratory. Due to the large number of spores captured, this method is labor-intensive, time-consuming, and inefficient, and sometimes leads to huge errors. Thus, an alternative method is required. In this study, a method was proposed to identify airborne disease spores from greenhouse crops using digital image processing. First, in an indoor simulation, images of airborne disease spores from three greenhouse crops were collected using portable volumetric spore traps. Then, a series of image preprocessing methods were used to identify the spores, including mean filtering, Gaussian filtering, OTSU (maximum between-class variance) method binarization, morphological operations, and mask operations. After image preprocessing, 90 features of the spores were extracted, including color, shape, and texture features. Based on these features, logistics regression (LR), K nearest neighbor (KNN), random forest (RF), and support vector machine (SVM) classification models were built. The test results showed that the average accuracy rates for the 3 classes of disease spores using the SVM model, LR model, KNN model, and RF model were 94.36%, 90.13%, 89.37%, and 89.23%, respectively. The harmonic average of the accuracy and the recall rate value (F value) were higher for the SVM model and its overall average value reached 91.68%, which was 2.03, 3.59, and 3.96 percentage points higher than the LR model, KNN model, and RF model, respectively. Therefore, this method can effectively identify 3 classes of diseases spores and this study can provide a reference for the identification of greenhouse disease spores.