Ion-adsorption rare earth mining areas are primarily situated in the hilly regions of southern China. However, mining activities have led to extensive deforestation of the original vegetation. The reclamation vegetation planted for ecological restoration faces significant challenges in surviving under environmental stresses, including heavy metal pollution, ammonia nitrogen contamination, and soil drought. To rapidly and accurately monitor the growth of reclamation vegetation, this study investigates the spectral variations and their impact on the accuracy of chlorophyll estimation, utilizing hyperspectral data and relative chlorophyll content (SPAD). Specifically, continuous–discrete wavelet transforms were applied, along with the original spectra and first derivative spectra, to enhance spectral anomalies in the reclamation vegetation and identify chlorophyll-sensitive spectral features. Additionally, multiple linear stepwise regression and backpropagation neural network models were employed to estimate chlorophyll content. The results revealed the following: (1) the d5 and d6 scales of the discrete wavelet effectively highlighted spectral anomalies in the reclamation vegetation; (2) Salix japonica (Salix fragilis L.), among typical reclamation species, exhibited poor adaptability to the environmental conditions of the rare earth mining area; (3) the backpropagation neural network model demonstrated superior performance in chlorophyll estimation, with the spectral features Fir, Fir_d4, Fir_d5, and Fir_d6 significantly enhancing the accuracy of the model, achieving an R2 of 0.93 for Photinia glabra (Photinia glabra (Thunb.) Maxim.). The application of continuous–discrete wavelet transforms to hyperspectral data significantly improves the precision of chlorophyll estimation, underscoring the potential of this method for the rapid monitoring of reclamation vegetation growth.