The invention relates to a construction method and application of a morphological fusion classification index of a neural image marker, and the construction method comprises the following steps: obtaining the structural MRI data of M centers, and extracting the feature data of a brain structure image; independently training the data of each center, respectively establishing a classification model of each center, and obtaining classification models of M centers; for any sample, calculating a classification weight value of the sample in each feature of each model in classification models of all centers, namely an SHAP matrix; and then taking the sample size used during training of each model as a weight, and calculating according to a formula (1) to obtain a single morphological fusion classification index MICI value: Si represents the sample size of the model i, B represents the total number of the features, ai represents the SHAP value of the feature a in the model i, and i = 1-M. The MICI value can well realize identification between mental disease patients and normal people, and has good interpretability, evolutionary property and expandability.