Accurate identification of the second and third compound leaf periods of soybean seedlings is a prerequisite to ensure that soybeans are chemically weeded after seedling at the optimal application period. Accurate identification of the soybean seedling period is susceptible to natural light and complex field background factors. A transfer learning-based Swin-T (Swin Transformer) network is proposed to recognize different stages of the soybean seedling stage. A drone was used to collect images of soybeans at the true leaf stage, the first compound leaf stage, the second compound leaf stage, and the third compound leaf stage, and data enhancement methods such as image rotation and brightness enhancement were used to expand the dataset, simulate the drone’s collection of images at different shooting angles and weather conditions, and enhance the adaptability of the model. The field environment and shooting equipment directly affect the quality of the captured images, and in order to test the anti-interference ability of different models, the Gaussian blur method was used to blur the images of the test set to different degrees. The Swin-T model was optimized by introducing transfer learning and combining hyperparameter combination experiments and optimizer selection experiments. The performance of the optimized Swin-T model was compared with the MobileNetV2, ResNet50, AlexNet, GoogleNet, and VGG16Net models. The results show that the optimized Swin-T model has an average accuracy of 98.38% in the test set, which is an improvement of 11.25%, 12.62%, 10.75%, 1.00%, and 0.63% compared with the MobileNetV2, ResNet50, AlexNet, GoogleNet, and VGG16Net models, respectively. The optimized Swin-T model is best in terms of recall and F1 score. In the performance degradation test of the motion blur level model, the maximum degradation accuracy, overall degradation index, and average degradation index of the optimized Swin-T model were 87.77%, 6.54%, and 2.18%, respectively. The maximum degradation accuracy was 7.02%, 7.48%, 10.15%, 3.56%, and 2.5% higher than the MobileNetV2, ResNet50, AlexNet, GoogleNet, and VGG16Net models, respectively. In the performance degradation test of the Gaussian fuzzy level models, the maximum degradation accuracy, overall degradation index, and average degradation index of the optimized Swin-T model were 94.3%, 3.85%, and 1.285%, respectively. Compared with the MobileNetV2, ResNet50, AlexNet, GoogleNet, and VGG16Net models, the maximum degradation accuracy was 12.13%, 15.98%, 16.7%, 2.2%, and 1.5% higher, respectively. Taking into account various degradation indicators, the Swin-T model can still maintain high recognition accuracy and demonstrate good anti-interference ability even when inputting blurry images caused by interference in shooting. It can meet the recognition of different growth stages of soybean seedlings in complex environments, providing a basis for post-seedling chemical weed control during the second and third compound leaf stages of soybeans.