Herbicide phytotoxicity represented a critical constraint on crop safety in soybean–corn intercropping systems, where early detection of herbicide stress is essential for implementing timely mitigation strategies to preserve yield potential. Current methodologies lack rapid, non-invasive approaches for early-stage prediction of herbicide-induced stress. To develop and validate a spectral-feature-based prediction model for herbicide concentration classification, we conducted a controlled experiment exposing three-leaf-stage vegetable soybean (Glycine max L.) seedlings to aqueous solutions containing three concentrations of nicosulfuron herbicide (0.5, 1, and 2 mL/L) alongside a water control. Hyperspectral imaging of randomly selected seedling leaves was systematically performed at 1, 3, 5, and 7 days post-treatment. We developed predictive models for herbicide phytotoxicity through advanced machine learning and deep learning frameworks. Key findings revealed that the ResNet-18 deep learning model achieved exceptional classification performance when analyzing the 386–1004 nm spectral range at day 7 post-treatment: 100% accuracy in binary classification (herbicide-treated vs. water control), 93.02% accuracy in three-class differentiation (water control, low/high concentration), and 86.53% accuracy in four-class discrimination across specific concentration gradients (0, 0.5, 1, 2 mL/L). Spectral analysis identified significant reflectance alterations between 518 and 690 nm through normalized reflectance and first-derivative transformations. Subsequent model optimization using this diagnostic spectral subrange maintained 100% binary classification accuracy while achieving 94.12% and 82.11% accuracy for three- and four-class recognition tasks, respectively. This investigation demonstrated the synergistic potential of hyperspectral imaging and deep learning for early herbicide stress detection in vegetable soybeans. Our findings established a novel methodological framework for pre-symptomatic stress diagnostics while demonstrating the technical feasibility of employing targeted spectral regions (518–690 nm) in field-ready real-time crop surveillance systems. Furthermore, these innovations offer significant potential for advancing precision agriculture in intercropping systems, specifically through refined herbicide application protocols and yield preservation via early-stage phytotoxicity mitigation.