Accurate estimations of carbon (C), nitrogen (N), and phosphorus (P) densities in shrublands are pivotal for assessing terrestrial ecosystem carbon sequestration. Combining in-situ investigations and machine learning facilitates large-scale patterns mapping, however, which often overlooks underlying ecological regulations. Here we utilize data from 1,122 survey plots across China's shrublands and develop a novel knowledge-based deep learning framework that integrates a structural equation model (SEM) to elucidate mechanisms and construct an artificial neural network (ANN) based on these causal relationships. Results show that biomass allocation to different organs follows allometric regulations and that N and P concentrations maintain a degree of stoichiometric homeostasis following biological stoichiometry theory. This insight guides the construction of our ANN, which outperforms both SEM and other prevalent machine learning methods. By leveraging ecological theories to inform model construction, our framework not only enhances prediction accuracy and explainability but also provides a methodological blueprint for ecological research.