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• A novel model (LabTNet) is proposed to estimate crop biochemical traits. • LabTNet jointly estimates multiple wheat traits by hyperspectral data. • LabTNet exhibits superior predictive performance than existing methods. • Grad-CAM analyzed hyperspectral attention regions of LabTNet. Accurate estimation of crop leaf and canopy biochemical traits, such as leaf dry matter content (Cm), leaf equivalent water thickness (Cw), leaf area index (LAI), dry leaf biomass (DLB), leaf total water content (LW), and fresh leaf biomass (FLB), is essential for monitoring crop growth accurately. The vegetation spectral feature technique combined with statistical regression methods is widely employed for remote sensing crop biochemical traits mapping. However, the crop canopy spectral reflectance is influenced by various crop biochemical traits and uncertainties in geometric changes of light and soil background effects. Consequently, the remote-sensing estimation of crop biochemical traits is limited. A potential solution involves training a deep learning model to understand the physical relationship between crop biochemical traits and canopy spectral reflectance based on a physical radiative transfer model (RTM). The primary focus of this study is to propose a winter-wheat leaf and canopy biochemical traits analysis and mapping method based on hyperspectral remote sensing, utilizing a deep learning network for leaf area index and leaf biochemical traits deep learning network (LabTNet). This study consists of four main tasks: (1) Field-based measurements of winter-wheat spectra and biochemical traits were conducted in two growing seasons. A PROSAIL RTM was also employed to generate a simulated dataset representing comprehensive and complex winter-wheat field conditions. (2) The LabTNet deep learning model was pre-trained using the simulated spectra dataset to acquire knowledge of the physical relationship between crop biochemical traits and canopy spectral reflectance derived from the RTM. Subsequently, the model was re-trained using the field-based spectra dataset from two growing seasons, employing a transfer learning technique. (3) An analysis was conducted to assess the performance of LabTNet against traditional statistical regression methods in estimating crop leaf and canopy biochemical traits. The study used the gradient-weighted class activation mapping (Grad-CAM) technique to analyze the attention regions of input spectra (454:8:950 nm, 960:10:1300 nm, 1450:10:1750 nm, 2000:10:2350 nm) by different convolutional neural network layers in LabTNet, aiming to enhance the interpretability of deep learning models. (4) Winter-wheat leaf and canopy biochemical traits (Cw, Cm, LAI, DLB, LW, and FLB) were mapped using the LabTNet deep learning model. Our research has the following conclusions: (1) Combining the RTM and deep learning techniques yields higher winter-wheat biochemical trait estimates than traditional statistical regression methods. (2) Different LabTNet deep learning model layers focus on distinct areas of canopy reflectance, corresponding to the sensitive regions for various winter-wheat biochemical traits. (3) LabTNet demonstrates similar winter-wheat leaf and canopy biochemical traits estimation performance using visible and near-infrared (VNIR) reflectance data and full-spectral (FS) range hyperspectral reflectance as inputs (Cw: R 2 = 0.603–0.653, RMSE = 0.0015–0.0015 cm; Cm: R 2 = 0.511–0.560, RMSE = 0.0006–0.0007 g/m2; LAI: R 2 = 0.773–0.793, RMSE = 0.65–0.66 m2/m2; LW: R 2 = 0.842–0.847, RMSE = 67.93–70.73 g/m2; DLB: R 2 = 0.747–0.762, RMSE = 21.10–21.89 g/m2; FLB: R 2 = 0.831–0.840, RMSE = 86.26–90.30 g/m2). The combined use of UAV hyperspectral remote sensing and the LabTNet model proves effective in providing high-performance winter-wheat leaf and canopy biochemical trait maps, offering valuable insights for agricultural management. [ABSTRACT FROM AUTHOR]