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The quality assurance of bulk medicinal materials, crucial for botanical drug production, necessitates advanced analytical methods. Conventional techniques, including high-performance liquid chromatography, require extensive pre-processing and rely on extensive solvent use, presenting both environmental and safety concerns. Accordingly, a non-destructive, expedited approach for assessing both the chemical and physical attributes of these materials is imperative for streamlined manufacturing. We introduce an innovative method, designated as Squeeze-and-Excitation Residual Network Combined Hyperspectral Image Analysis (SE-ReHIA), for the swift and non-invasive assessment of the chemical makeup of bulk medicinal substances. In a demonstrative application, hyperspectral imaging in the 389–1020 nm range was employed in 187 batches of <i>Salvia miltiorrhiza</i>. Notable constituents such as salvianolic acid B, dihydrotanshinone I, cryptotanshinone, tanshinone IIA, and moisture were quantified. The SE-ReHIA model, incorporating convolutional layers, maxpooling layers, squeeze-and-excitation residual blocks, and fully connected layers, exhibited <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>R</mi></mrow><mrow><mi>c</mi></mrow><mrow><mn>2</mn></mrow></msubsup></mrow></semantics></math></inline-formula> values of 0.981, 0.980, 0.975, 0.972, and 0.970 for the aforementioned compounds and moisture. Furthermore, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>R</mi></mrow><mrow><mi>p</mi></mrow><mrow><mn>2</mn></mrow></msubsup></mrow></semantics></math></inline-formula> values were ascertained to be 0.975, 0.943, 0.962, 0.957, and 0.930, respectively, signifying the model’s commendable predictive competence. This study marks the inaugural application of SE-ReHIA for Salvia miltiorrhiza’s chemical profiling, offering a method that is rapid, eco-friendly, and non-invasive. Such advancements can fortify consistency across botanical drug batches, underpinning product reliability. The broader applicability of the SE-ReHIA technique in the quality assurance of bulk medicinal entities is anticipated with optimism.