A super-hydrophobic micro-pit array chip, a preparation method therefor, and applications thereof. The micro-pit array chip comprises a micro-pit array layer, and the surface on which micro-pits are formed, of the micro-pit array layer is a super-hydrophobic surface except micro-pits or the bottoms of the micro-pits. The micro-pit array chip may be: 1) the surface except the micro-pits is the super-hydrophobic surface, and the micro-pit array chip comprises the micro-pit array layer and a super-hydrophobic layer attached to the surface of the micro-pit array layer; and 2) the surface except the bottoms of the micro-pits is a super-hydrophobic surface, the micro-pit array layer comprises a substrate layer and a micropore array layer attached to the surface of a substrate, and micropore array layer is made of a super-hydrophobic material. By means of the micro-pit array chip, complete isolation among cell microarrays can be implemented at a very low cost in the cell microarray construction process, cross contamination among cell arrays is avoided, good biocompatibility is ensured, and the micro-pit array chip has no obvious impact on normal growth of various cells and is suitable for high-throughput cell detection and analysis.