Sunflower is an important crop, and the vitality and moisture content of sunflower seeds have an important influence on the sunflower’s planting and yield. By employing hyperspectral technology, the spectral characteristics of sunflower seeds within the wavelength range of 384–1034 nm were carefully analyzed with the aim of achieving effective prediction of seed vitality and moisture content. Firstly, the original hyperspectral data were subjected to preprocessing techniques such as Savitzky–Golay smoothing, standard normal variable correction (SNV), and multiplicative scatter correction (MSC) to effectively reduce noise interference, ensuring the accuracy and reliability of the data. Subsequently, principal component analysis (PCA), extreme gradient boosting (XGBoost), and stacked autoencoders (SAE) were utilized to extract key feature bands, enhancing the interpretability and predictive performance of the data. During the modeling phase, random forests (RFs) and LightGBM algorithms were separately employed to construct classification models for seed vitality and prediction models for moisture content. The experimental results demonstrated that the SG-SAE-LightGBM model exhibited outstanding performance in the classification task of sunflower seed vitality, achieving an accuracy rate of 98.65%. Meanwhile, the SNV-XGBoost-LightGBM model showed remarkable achievement in moisture content prediction, with a coefficient of determination (R2) of 0.9715 and root mean square error (RMSE) of 0.8349. In conclusion, this study confirms that the fusion of hyperspectral technology and multivariate data analysis algorithms enables the accurate and rapid assessment of sunflower seed vitality and moisture content, providing robust tools and theoretical support for seed quality evaluation and agricultural production practices. Furthermore, this research not only expands the application of hyperspectral technology in unraveling the intrinsic vitality characteristics of sunflower seeds but also possesses significant theoretical and practical value.