The invention discloses a preparation method of a microarray chip. The method comprises the steps of target chip selection, auxiliary chip selection, chip docking, chip separation and the like, mother liquor droplets and buffer solution droplets of the surface of a target chip and the surface of an auxiliary chip are manipulated to be fused and split, the components in corresponding droplets are changed, and the obtained target chip is the microarray chip, target droplets are adsorbed on the hydrophilic region of the microarray chip, and the target droplets serve as a droplet array composed of multiple droplets with different components. According to the preparation method of the microarray chip, multiple droplets can be manipulated simultaneously to conduct fusion and separation, the droplet microarrays of concentration gradient, mechanical gradient, multicomponent chemistry, cell density, anisotropic gel and the like are formed, and broad prospects of preparation aspects on biological analysis and gel droplets are achieved.