The classification of certain agricultural species poses a formidable challenge due to their inherent resemblance and the absence of dependable visual discriminators. The accurate identification of these plants holds substantial importance in industries such as cosmetics, pharmaceuticals, and herbal medicine, where the optimization of essential compound yields and product quality is paramount. In response to this challenge, we have devised an automated classification system based on deep learning principles, designed to achieve precision and efficiency in species classification. Our approach leverages a diverse dataset encompassing various cultivars and employs the Parallel Artificial Multiple Intelligence System–Ensemble Deep Learning model (P-AMIS-E). This model integrates ensemble image segmentation techniques, including U-Net and Mask-R-CNN, alongside image augmentation and convolutional neural network (CNN) architectures such as SqueezeNet, ShuffleNetv2 1.0x, MobileNetV3, and InceptionV1. The culmination of these elements results in the P-AMIS-E model, enhanced by an Artificial Multiple Intelligence System (AMIS) for decision fusion, ultimately achieving an impressive accuracy rate of 98.41%. This accuracy notably surpasses the performance of existing methods, such as ResNet-101 and Xception, which attain 93.74% accuracy on the testing dataset. Moreover, when applied to an unseen dataset, the P-AMIS-E model demonstrates a substantial advantage, yielding accuracy rates ranging from 4.45% to 31.16% higher than those of the compared methods. It is worth highlighting that our heterogeneous ensemble approach consistently outperforms both single large models and homogeneous ensemble methods, achieving an average improvement of 13.45%. This paper provides a case study focused on the Centella Asiatica Urban (CAU) cultivar to exemplify the practical application of our approach. By integrating image segmentation, augmentation, and decision fusion, we have significantly enhanced accuracy and efficiency. This research holds theoretical implications for the advancement of deep learning techniques in image classification tasks while also offering practical benefits for industries reliant on precise species identification.