A novel micro-channels thermosyphon technology for passively cooling 3D stacked chips was provided, and the thermosyphon boiling characteristics in vertical and inclined micro-channels with two open ends which simulate the specific stacked structure of actual 3D chip were experimentally carried out. In order to improve the heat transfer by surface treatment technology, four nanoparticles (CuO, Cu, Al2O3, SiO) were added to the base fluids to make nano-structure coatings on the heater surfaces by using a long time pool boiling treatment. Then, micro-channel thermosyphon boiling experiments were carried out with four kinds of working liquids: two pure fluids (deionized water and R113) and two moist fluids (deionized water+surfactant and R113+surfactant). The gaps and heights of micro-channels tested were in the range of 30 µm to 60 µm and 30 mm to 90 mm, respectively. Experimental results show that nano-structure coatings can significantly enhance both the maximum heat flux and heat transfer coefficient of thermosyphon boiling in micro-channels, and exist both the optimal nanoparticles kind and nanoparticles concentration in the base fluids. The experimental results provided some meaningful technology support for 3D stacked chip cooling.