The invention relates to the technical field of biology, in particular to a tissue microarray of decidua and villi pairing, a preparation method and application thereof. The tissue microarray is prepared with the decidua and villus specimens of a normal pregnancy woman or a pathologic pregnancy patient arranged in sample application holes, so that pairing is formed between the decidua tissue and the villus tissue from the same specimen, and the functional presentation of the maternal-fetal interface of a physiological structure onto the tissue microarray is achieved. The tissue microarray has the advantages that high throughput is achieved, plenty of information is obtained in one time, and the efficiency is improved by hundreds of times; parallelization is achieved, the comparability is high, and the precision is high; the experimental error is small, and experimental conditions remain the same; convenience is brought to arrangement of various kinds of experimental control, and the research cost is greatly reduced. The tissue microarray can be used for etiology screening and molecular typing of pathologic pregnancy, screening and verifying of a novel marker, screening of individual treatment patients, judgment of a therapeutic effect and prognosis and the like, and the tissue microarray has important significance for the research of a normal pregnancy maintaining mechanism and pathologic pregnancy pathogenesis.