The present invention discloses a spatial three-dimensional genomics sequencing method based on a microfluidic chip and its applications. The process of molecular labeling of tissue sections is segmented into steps: "overall labeling - partial lysis - partial labeling - overall lysis." This method sequentially performs spatial information labeling at the micron level and protein-DNA complex labeling at the nanometer level. It effectively integrates resolution from the visual micron scale to the invisible base length scale. This method can be applied to the development or preparation of products for disease detection or for observing organ development.