This study constructs a model for the rapid identification of the origins of edible sunflower (Helianthus) using Kernel Extreme Learning Machine (KELM) with multi-source information fusion technology. Near-infrared spectroscopy (NIRS) and nuclear magnetic resonance spectroscopy (NMRS) were utilized to analyze 180 sunflower samples from the Xinjiang, Heilongjiang, and Inner Mongolia regions. Initially, the identification models for the origin of sunflowers using NIR and NMR data were compared between two algorithms: the Extreme Learning Machine (ELM) and KELM, combined with various spectral preprocessing methods. The experiment found that the NIR spectral model preprocessed with standard normal variate (SNV) using the KELM algorithm was the most accurate, achieving accuracies of 98.7% in the training set and 97.2% in the test set. The spin-echo NMR spectral model preprocessed with non-local means (NLMs) using the KELM algorithm was the second best, with accuracies of 98.4% in the training set and 96.4% in the test set. To further improve the accuracy of the identification models, innovative sunflower origin identification models were developed based on data layer fusion and feature layer fusion using NIRS and NMRS. In the data layer fusion model, the KELM algorithm model was optimal, achieving a test set accuracy and F1 score of 98.2% and 98.18%, respectively, an improvement of 1.0% over the best single data source model. In the feature layer fusion model, four types of feature-layer information-fusion identification models were established using two feature extraction algorithms, Competitive Adaptive Reweighted Sampling (CARS) and Variable Importance Projection (VIP), combined with joint feature and simple merging feature strategies. The CARS-KELM algorithm combined with the joint feature method was found to be the best, achieving 100% accuracy in both the training and test sets, an improvement of 2.8% over the best single data source model. Identifying the origin of edible sunflower using NIRS and NMRS is demonstrated as feasible by the results. The best single-spectrum sunflower origin identification model was achieved using the KELM algorithm with SNV preprocessing. The feature layer fusion method combining NIRS and NMRS data is suitable for handling the task of sunflower origin identification. This method significantly improves the recognition accuracy of the model compared to a single model, achieving fast and accurate origin identification of edible sunflowers. The research results provide a new method for rapid identification of sunflower origin.