The leaf chlorophyll content (LCC) of winter wheat, an important food crop widely grown worldwide, is a key indicator for assessing its growth and health status in response to CO
2 stress. However, the remote sensing quantitative estimation of winter wheat LCC under CO
2 stress conditions also faces challenges such as an unclear spectral sensitivity range, baseline drift, overlapping spectral peaks, and complex spectral response due to CO
2 stress changes. To address these challenges, this study introduced the fractional order derivative (FOD) and continuous wavelet transform (CWT) techniques into the estimation of winter wheat LCC. Combined with the raw hyperspectral data, we deeply analyzed the spectral response characteristics of winter wheat LCC under CO
2 stress. We proposed a stacking model including multiple linear regression (MLR), decision tree regression (DTR), random forest (RF), and adaptive boosting (AdaBoost) to filter the optimal combination from a large number of feature variables. We use a dual-band combination and vegetation index strategy to achieve the accurate estimation of LCC in winter wheat under CO
2 stress. The results showed that (1) the FOD and CWT methods significantly improved the correlation between the raw spectral reflectance and LCC of winter wheat under CO
2 stress. (2) The 1.2-order derivative dual-band index (RVI (R
720, R
522)) constructed by combining the sensitive spectral bands of the CO
2 response of winter wheat leaves achieved a high-precision estimation of the LCC under CO
2 stress conditions (R
2 = 0.901). Meanwhile, the red-edged vegetation stress index (RVSI) constructed based on the CWT technique at specific scales also demonstrated good performance in LCC estimation (R
2 = 0.880), verifying the effectiveness of the multi-scale analysis in revealing the mechanism of the CO
2 impact on winter wheat. (3) By stacking the sensitive spectral features extracted by combining the FOD and CWT methods, we further improved the LCC estimation accuracy (R
2 = 0.906). This study not only provides a scientific basis and technical support for the accurate estimation of LCC in winter wheat under CO
2 stress but also provides new ideas and methods for coping with climate change, optimizing crop-growing conditions, and improving crop yield and quality in agricultural management. The proposed method is also of great reference value for estimating physiological parameters of other crops under similar environmental stresses.
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