The Chinese mitten crab (Eriocheir sinensis) is highly valued by consumers for its delicious taste and high nutritional content, including proteins and trace elements, giving it significant economic value. However, variations in taste and nutritional value among crabs from different regions lead to considerable price differences, fueling the prevalence of counterfeit crabs in the market. Currently, there are no rapid detection methods to verify the origin of Chinese mitten crabs, making it crucial to develop fast and accurate detection techniques to protect consumer rights. This study focused on Chinese mitten crabs from different regions, specifically Hongze Lake, Tuo Lake, and Weishan Lake, by collecting near-infrared (NIR) diffuse reflectance spectral data from both the abdomen and carapace regions of the crabs. To eliminate noise from the spectral data, pretreatment was performed using Savitzky–Golay (SG) smoothing, Standard Normal Variate (SNV) transformation, and Multiplicative Scatter Correction (MSC). Key wavelengths reflecting the origin of Chinese mitten crabs were selected using Competitive Adaptive Reweighted Sampling (CARS), Bootstrap Soft Shrinkage (BOSS), and Uninformative Variable Elimination (UVE) algorithms. Finally, Support Vector Machine (SVM), Convolutional Neural Network (CNN), and Back Propagation Neural Network (BP) models were developed for rapid detection of crab origin. The results demonstrated that MSC provided the best preprocessing performance for NIR spectral data from both the abdomen and back of the crabs. For abdomen data, the SVM model developed using feature wavelengths selected by the CARS algorithm after MSC preprocessing achieved the highest accuracy (Acc) of 90.00%, with precision (P), recall (R), and F1-score for crabs from Weishan Lake at 89.29%, 86.21%, and 87.72%, respectively; for crabs from Tuo Lake at 86.96%, 95.24%, and 90.91%; and for crabs from Hongze Lake at 90.00%, 93.10%, and 91.53%. For carapace data, the SVM model based on wavelengths selected by the BOSS algorithm after MSC pretreatment achieved the best performance, with an Acc of 87.50%, and P, R, and F1 for crabs from Weishan Lake at 77.14%, 93.10%, and 84.38%; for Tuo Lake crabs at 100%, 90.47%, and 95.00%; and for Hongze Lake crabs at 92.31%, 80.00%, and 85.71%. In conclusion, NIR spectroscopy can effectively detect the origin of Chinese mitten crabs, providing technical support for developing rapid detection instruments and thereby safeguarding consumer rights.