The invention relates to an immunoliposome biochip, a preparation method thereof and an application thereof in biological detection. The immunoliposome provided by the invention is distributed on the chip in a micro-array way, and includes molecule probes, such as molecular beacon with fluorescence; and outside of the immunoliposome is loaded with various ligands. The immunoliposome biochip can specifically capture target cells in a cell mixture, and ensure messenger RNA and/or micromolecule RNA in the target cells without destroying biomarkers in the cells. In addition, the immunoliposome biochip provided by the invention can be used for capturing and selecting nanoparticles secreted by virus and cells, such as micro bubbles and exosomes. The immunoliposome biochip has advantages of simple operation, low cost, rapidness, sensitive and high selectivity, and can be used for molecular detection of various diseases, food safety and other fields.