The invention relates to a decidua and villus pairing cDNA chip. The cDNA chip is prepared through the following method that the decidua and villus tissue of a woman with early pregnancy abortion are taken, the RNA is extracted, cDNA is formed by reverse transcription and preset in a PCR reaction plate, and cDNA chip is made. A preparation method and application of cDNA chip are further provided. The method and application have the advantages that the decidua and villus tissue of every abortion woman are respectively taken, pairing is formed by cDNA, the cDNA pairs are concentrated on the same chip, and the function presentation of parent-fetal interface of the physiological structure is achieved on the chip outside the body. The decidua and villus pairing cDNA chip has the advantages of being high in throughput, strong in specificity, high in sensitivity, simple and fast in operation, high in quantitative accuracy, strong in result reliability, simple in result analysis, complete in clinical information for samples and the like, and the cDNA chip can be used for quantitative detection of the expression statuses of a target gene in different patients and for conducting in-depth correlation analyses of clinical information.