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 Salvia miltiorrhiza. 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 Rc2 values of 0.981, 0.980, 0.975, 0.972, and 0.970 for the aforementioned compounds and moisture. Furthermore, Rp2 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.