The invention relates to a two-layer cell culture system organ chip and a preparation method thereof. The organ chip comprises a two-layer cell culture system, wherein each layer comprises a culture solution micro-fluid channel, a medicament micro-fluid channel, cell culture chambers and a medicament testing tank; a micro structure and micro-fluid channels are designed on the organ chip, two cells are respectively fixed on each specific cell culture chamber, and intercellular signal transmission and interaction between the cells are performed by virtue of the micro-fluid channels. The organ chip realizes the parallel implantation and co-culture of two or more cells, is simple in operation, reduces the dose of practical samples, simplifies the cell implantation process, has the characteristics of portability, economic performance, high efficiency and accuracy, and can be used for independently performing cell seeding and culture and detection of medicament toxicity or pharmacological activity. The two-layer cell culture system organ chip is a novel organ chip with miniaturization, automation and visualization, prepared by simulating the structures and functions of a human organ, and can be used for providing the effective theoretical basis for tissue and regeneration engineering, organ transplantation and medicament evaluation.