Subthreshold depression, a transition state to depression, seriously hinders the early diagnosis of depression. Current studies mostly use heterogeneous definitions of subthreshold depression, making the results of such meta-analyses questionable. Therefore, it is of vital significance to develop an objective method for the diagnosis of subthreshold depression based on objective criteria. In traditional Chinese medicine (TCM), symptoms similar to subthreshold depression have been extensively explored. However, diagnostic methods in TCM still depend heavily on the experience of doctors and lack integration with modern diagnostic techniques, which makes it challenging to explain the pathogenesis of subthreshold depression. Consequently, we propose an explainable framework, based on a stacking ensemble algorithm, for subthreshold depression recognition from biomarkers in the pulse waveform and concepts of pulse in TCM. In this method, Naive Bayes, Random Forest, Extremely Randomized Trees, Categorical Boosting and Logistic Regression are chosen as basic learners, and XGBoost is selected as the meta-classifier. Based on the five-fold cross-validation method, grid search method and repetition of training, the stacking ensemble model shows superiority on most performance evaluation metrics including AUC, F1 scores, MCC, precision and sensitivity. Besides, by analyzing the Adjusted Odds Ratio of features in the pulse waveform, we obtained four features that have a high correlation with the occurrence of subthreshold depression and derived physiological changes in patients with subthreshold depression based on their physiological significance.